Live coverage of the service, which aired on Saturday (February 18) between 5pm and 8.30pm, prompted 118 complaints that the coverage was too extensive, with a further 34 upset that the service was interrupted before the end.
The BBC released a statement saying: "This was the funeral of a recording artist who had a substantial impact on late 20th century music and whose death had come as a great shock to the wider music industry and to her millions of fans.
"This was reflected in our viewing figures and they show that the coverage of the funeral drove significantly higher audiences for the News Channel during this period compared to the rest of Saturday.
"The funeral service lasted significantly longer than any broadcaster expected, and as we had committed to the coverage it would not have been appropriate to opt out of the service any earlier than we did.
"We recognise that the duration of the coverage was too long for some viewers, but we kept the news ticker going on screen throughout and those who wanted other news of the day could have turned over to BBC One for the main tea time bulletin there. The website and mobile app services were also running as normal, as were the BBC radio bulletins."
The corporation added: "We are sorry if this wasn't to the satisfaction of all our viewers but it is part of the News Channel function to be there when major stories take place, and we felt that this was such an occasion."
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Watch Whitney Houston's casket arrive at New Hope Baptist Church in Newark for her funeral: