The TV and radio star, 66, has hosted the Sunday evening 5 to 7pm slot for almost 13 years, but a schedule change now sees him share the space with comedian Rob Beckett.
The duo will present their shows alternately, each for 13 weeks at a time, which O'Grady has said was a "management decision".
Some listeners had complained about the change.
Responding on the complaints section of their website, the BBC said: “Paul is much-loved by many of our listeners, and whilst we’re making this change to Sunday afternoons, he very much remains a firm favourite here in Wogan House.
"We’ve changed the broadcast pattern of Paul’s show so that he’s now on air for two 13 week series each year. This doesn’t significantly alter the number of shows he’s been signed up to do on Radio 2, but having this consistent pattern will make it a lot easier for us to signpost for listeners when he’s on air.
"Rather than have a range of deputies host the show throughout the year, we’ll now have Rob Beckett on Sunday afternoons with his own series, alternating with Paul’s.”
The statement went on to say that plans do “evolve”.
It said: “We understand that listeners never want their favourite bits of the Radio 2 schedule to change, but our plans do evolve over time, and that’s the case here.”
O’Grady hosted his last show on February 13 and told his fans on Instagram that it was his last for “quite some time”.
He said: “There’s a new regime now, I do 13 weeks on and then 13 off which is nothing to do with me as it’s a management decision."
He said he should be back in May.
Additional reporting by PA.
Watch: Paul O'Grady admits he's bored of his teatime chat show