The BBC was made aware of a police investigation into DJ Scott Mills in 2017, the corporation has confirmed.
But the Radio 2 presenter was sacked after "new information" about his conduct came to light in recent weeks, the BBC said.
Mills was investigated by police over historical allegations of serious sexual offences in 2016, but no charges were brought after prosecutors decided in 2019 there was insufficient evidence to proceed with the case.
Mills has not yet responded to repeated requests for comment.
On Tuesday, the Metropolitan Police told BBC News that the teenage boy at the centre of the sexual offences investigation was under the age of 16.
BBC News understands that the director general at the time of the investigation, Tony Hall, did not know about the allegations.
The BBC's statement on Wednesday came after mounting pressure on the broadcaster to explain what led to the Radio 2 DJ's sudden departure.
In a statement, a BBC spokesperson said: "Scott Mills had a long career across the BBC, he was hugely popular and we know the news this week has come as a shock and surprise to many.
"We also recognise there's been much speculation in the media and online since Monday. We hope people understand that there is a limit to what we can say because we have to be mindful of the rights of those involved.
"What we can confirm is that in recent weeks, we obtained new information relating to Scott and we spoke directly with him. As a result, the BBC acted decisively in line with our culture and values and terminated his contracts on Friday 27 March."
The spokesperson added: "Separately, we can confirm the BBC was made aware in 2017 of the existence of an ongoing police investigation, which was subsequently closed in 2019 with no arrest or charge being made. We are doing more work to understand the detail of what was known by the BBC at this time."
The statement concluded that the BBC has made "a significant commitment to improve its culture, processes and standards".
"Last year, following an independent culture review, we set out the behavioural expectations for everyone who works with or for the BBC and we were clear action would be taken if these were not met."
On Monday, it was announced that the former Radio 1 presenter had been sacked by the BBC over allegations related to his personal conduct.
At the time, the BBC did not give any further details over the allegations and it is not clear what, if any, role the police investigation played in his sacking.
The 53-year-old was questioned in 2018 over historical allegations of serious sexual offences. But the investigation, which began in 2016, was closed in 2019 after the Crown Prosecution Service deemed there was insufficient evidence to bring charges.
The allegations, first published on Monday by the Mirror, relate to the period between 1997 and 2000, police said, when Mills would have been in his mid-twenties.
On Tuesday, the BBC apologised for not looking into a separate allegation of "inappropriate communications" involving Mills, first reported in the Telegraph, raised by a freelance journalist last year.
The BBC said: "We received a press query in 2025 which included limited information. This should have been followed up and we should have asked further questions. We apologise for this and will look into why this did not happen."
Mills's last Radio 2 breakfast show appearance was on Tuesday 24 March, when he signed off by saying: "Back tomorrow."
DJ Gary Davies started the show the following day by saying he was "in for Scott Mills", and has been covering the breakfast show since.
Davies and Radio 2's overnight presenter OJ Borg will cover the show over the next week, as speculation begins to mount over who will replace Mills.
Mills joined Radio 2's weekday schedule in 2022 when he replaced Steve Wright as the host of the afternoon show. He was promoted to breakfast in January 2025.
Prior to his work on Radio 2, Mills was a mainstay on Radio 1 - which he joined in 1998 - for decades.
He competed on Strictly Come Dancing in 2014, and more recently provided TV commentary for BBC One on the semi-finals of Eurovision with Rylan Clark.
In 2024, Mills and his husband Sam won the BBC competition series Celebrity Race Across The World. Mills was last seen on TV in March on a Traitors skit during Comic Relief.
Mills was due to host a new video podcast that will accompany the new series of Race Across The World, which begins on Thursday.
According to Deadline, the BBC plans to go ahead with the podcast once it appoints a new host. The BBC has been asked for comment.
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