The award was presented by comedy legend Sir Ken Dodd, who joked that the arena was a "magnificent shed" before reading out the nominees and eventual winner.
The comedy programme's, Brendan O'Carroll, thanked the public for voting and made a reference to Sir Ken's accidental reading out of Mrs Brown's Boys twice in the run up to the reveal.
O'Carroll, joined by the cast and crew of the BBC sitcom, said: "Thank you so much, we're all here ... thank you Sir Ken, to be nominated twice in the same category is amazing, we so appreciate it.
"Thank you so much to all of you who voted, it's really important that you vote, this is the most important award we get.
"It's very, very exciting and very humbling. Thanks to the BBC and everyone involved."
The Great British Bake Off's Mary Berry won the TV judge prize, beating another recently-departed judge Len Goodman to the honour.
The TV veteran, who stood down from her role as a judge on the popular cookery programme due to its move from the BBC to Channel 4, also beat The X Factor and Britain's Got Talent's Simon Cowell, BGT's David Walliams and The X Factor's Nicole Scherzinger.
Strictly Come Dancing's Goodman finished his 12-year tenure on the dancing show's panel in December.
A stunned Berry, 81, was cheered by the audience gathered at London's O2 Arena as she took to the stage with the help of host Dermot O'Leary before accepting the award, which was voted for by the public.
She said: "I'm thrilled ... I love judging, it has always been a great honour.
"I think I know how to bake and I love telling people that, next time, do a little bit better.
"But the greatest reward is that all the young are baking and everybody is sitting down at 8pm, the whole family: gran, the baby in arms. There is no swearing, it's the best programme, and I'm so grateful, and thank you very much."
TV duo Ant and Dec were named as the first winners of the night at the NTAs, scooping the entertainment programme prize for their show Saturday Night Takeaway, beating other popular shows such as The Graham Norton Show and Keith Lemon's Celebrity Juice.
Accepting the award, Ant said: "It really is our baby and, it's a bit of a shock first award up, but what a thrill."
Dec said: "Thank you, thank you so much, thank you to all of the talented clever people that stand behind us here and come up with all the ideas and all that. We have such fun doing it and thrilled you like watching it.
"We're back at the end of February for another run."
Long-running BBC medical drama Casualty beat big hitters such as Game Of Thrones, The Night Manager and Happy Valley to be named the winner of the drama category.
Collecting the award on stage with members of the cast and crew, actress Amanda Mealing said: "Thank you very, very much all of you that voted for us, we've been going for 30 years, some of you have been watching from the very start and some of you are new. You are strong, you are true, you are faithful."
Her co-star Cathy Shipton said the win was a wonderful way to celebrate the show's 30th anniversary, adding: "Thank you all for keeping us there."
EastEnders star Lacey Turner won the coveted serial drama performance award.
The actress, who plays Stacey Slater, fought back tears as she took to the stage.
She said: "Oh my goodness. I was so sure I was staying in my seat. Thank you so much to everybody who voted, who supported me over the last 12 years. I can't tell you how much it means."
After thanking her family and friends, she added: "Most of all thank you to all of those people sitting over there, it is so, I feel so lucky to wake up every day and love my job. I really am part of a team, a community, one big family, and for that I really am proud.
"This one's for the Fowlers, thank you!"
Channel 4's hit show, Gogglebox, can also celebrate a win as they took home the gong in the factual entertainment category.
ITV quiz show The Chase was named the winner of the daytime category.
The show's host, Bradley Walsh, dedicated the win to a member of the team who had died last year.
Walsh said: "Thank you very much, it's an absolute honour, the show goes from strength to strength."
The television presenter also joked about sharing the same stage as funnyman Sir Ken, quipping that he first worked with him during the Royal Variety Performance, adding: "Queen Victoria loved every second of it."
Good Morning Britain presenters Susanna Reid and Piers Morgan presented the award and Morgan walked on stage alongside Reid with a gag on his mouth.
Reid explained: "It's been a controversial week on Good Morning Britain, we've had tears, we've had tantrums, we've even had a walkout. So I've done what people have been urging me to do for quite some time - I have finally gagged Piers Morgan."
Call The Midwife was crowned the winner of the period drama award over rivals Stranger Things, Peaky Blinders, Poldark and Victoria.
The BBC series became the first recipient of the award as it is a new category this year.
Call The Midwife's executive producer Pippa Harris said: "Thank you, thank you so much, this is a huge, huge honour for all of us, I wanted to say a few thanks yous to the NTAs, to everyone who voted, a huge thank you to the BBC, and also to our tireless cast and crew who work so brilliantly on the show to make it the best it can possibly be.
"I want to single out three women who have been inspirational: the first is Jennifer Worth whose memoirs inspired the drama, our producer Ann Tricklebank, and back at home with toothache poor Heidi Thomas who is our inspiration. She writes the scripts and it is her passion and compassion that is on the page in every scene of the drama."
Harris said it was important for Call The Midwife to represent women's issues in a time that they are "being marginalised and ignored", and praised the programme for relating to people today despite it being set in the 1950s and 1960s.
This Morning was named the winner of the live magazine category.
The team of the ITV show took to the stage, where host Phillip Schofield referenced he and Holly Willoughby's alcoholic antics last year, saying that instead this year they were going to celebrate by getting tattoos.
Last year the duo arrived to present This Morning still wearing their NTA outfits, after getting very boozy at the awards show the previous night.
Schofield started his thank you speech by remembering the show's agony aunt, Denise Robertson, who died early in 2016.
Willoughby said: "What are you doing to us you crazy people, thank you so much. We love, love, love doing this show, we really do, it's so special.
"I love working with Phillip every day and I'm so lucky to sit next to my best friend all the time. Thank you so much."
Schofield added: "We just want to say obviously we shamed ourselves last year and so we are not going to do that again this year, we are going to get tattoos. Thank you very much."
Here is a full list of winners:
:: Entertainment Programme: Ant and Dec's Saturday Night Takeaway
:: Drama Performance: Sarah Lancashire
:: Factual Entertainment: Gogglebox
:: Serial Drama Performance: Lacey Turner (EastEnders)
:: Comedy: Mrs Brown's Boys
:: TV Judge: Mary Berry
:: Daytime: The Chase
:: Period Drama: Call The Midwife
:: Live Magazine: This Morning
:: Newcomer: Faye Brookes (Coronation Street)
:: TV Presenter: Ant and Dec
:: Special Recognition - Graham Norton
:: Drama - Casualty
:: Challenge Show - I'm a Celebrity! Get Me Out of Here!
:: Serial Drama - Emmerdale
:: Talent Show - Strictly Come Dancing