In a complaint report published on Friday, the corporation said some viewers had also expressed that they felt the story should have “focused more on the Illegal Migration Bill and criticism it has received”.
Lineker, 62, was briefly suspended as host of Match Of The Day this month over his criticism of the Government’s asylum policy on Twitter but returned to air following a boycott by top on-air talent at the broadcaster.
Pundits and presenters dropping out of a host of football shows in solidarity with Lineker prompted two days of disruption to TV and radio schedules.
The BBC has said it believes its coverage of the story was “proportionate, fair and duly impartial”.
In a statement, it added: “The row over Gary Lineker’s social media use, with regards to the BBC Editorial Guidelines, generated high media interest, as well as reaction from politicians from across the political spectrum and sporting personalities; this also caused disruption to the BBC Sport scheduling over the weekend of Mr Lineker’s suspension.
“This was a story of significance and we legitimately reported on the impact for the BBC and Mr Lineker.
“However, we continued to report on many other stories of national and international importance, including the cost-of-living crisis and the collapse of US Silicon Valley Bank.”
The broadcaster also stated its coverage included context explaining Lineker’s criticism of the Government’s new asylum policy and that they have separately reported on the Bill including “a wide range of views from those both critical and supportive of the proposals”.
However, they argued that it was “primarily a media story” which is why their focus was on the discussions it raised around freedom of speech and impartiality at the BBC.
The episode of BBC’s Sunday With Laura Kuenssberg, which aired over the weekend of disruption, also received particular complaints from people who felt the programme “displayed bias against Gary Lineker”.
“Throughout the programme we looked at the issues highlighted by the row over Gary Lineker’s social media use and the BBC Editorial Guidelines in detail, hearing a range of nuanced views, some of which were supportive of Gary Lineker,” a statement from the corporation said.
Two messages from viewers read out at the end of the programme were particularly referenced in the complaints but the broadcaster argued this was “one aspect” of their overall coverage which they feel “offered fair and duly impartial analysis of what this signified for Gary Lineker and the BBC, and the wider political implications”.
The BBC also issued an apology after they received complaints from those disappointed with the disruption to the broadcaster’s football schedule during the weekend of turbulence.
“We’re sorry for the disruption to our schedules,” it said.
“We know how much our audiences value our football programming and we worked hard to keep it on air on the 11 and 12 March. We’re glad that our normal coverage is now back.
“We’d like to reassure all audiences that this disappointment has been heard and discussed at a senior level.”
Lineker was taken off air after comparing the language used to launch the new Government asylum seeker policy with 1930s Germany in a tweet.
BBC director-general Tim Davie later said he recognised “grey areas” in the broadcaster’s social media guidance could cause “confusion” and announced an independent review of the guidelines, particularly for freelancers.
MPs will also question a former BBC director general, Lord Birt, and former BBC chairman, Lord Patten of Barnes, on the broadcaster’s impartiality at a Digital, Culture, Media and Sport committee meeting next week.