Frank-Juergen Weise told newspaper Bild An Sonntag: “We’re preparing for 250,000 to 300,000 refugees this year.”
He added that if more people were to come, his office would come under pressure but suggested he was not worried about such a scenario, saying it was instead likely that fewer than 300,000 would come this year.
Germans tend to use the word refugee to refer to both refugees and migrants who are seeking protection but do not have refugee status.
The comments come hours after German Vice Chancellor Sigmar Gabriel said that ChancellorAngela Merkel’s conservatives had “underestimated” the challenge of integrating a record number of migrants.
Gabriel is also leader of the Social Democrats (SPD) – the junior coalition partner in Merkel’s government – and his comments to broadcaster ZDF come as campaigning gets under way for a federal election next year.
More than one million migrants arrived in Germany from the Middle East, Africa and elsewhere last year.
Mr Gabriel said: “I, we always said that it’s inconceivable for Germany to take in a million people every year.”
The IAB German labour office research institute says around 16,000 are still arriving each month, compared with more than 200,000 in November.
Mr Gabriel also criticised Merkel’s catchphrase “Wir schaffen das”, meaning “We can do this”, which she adopted during the migrant crisis last summer and has repeatedly used since.
The German Chancellor used the phrase at a news conference she held in late July after a spate of attacks on civilians in Germany, including two claimed by Islamic State, that have put her open-door migrant policy in the spotlight.
More than one million migrants arrived in Germany last year
Merkel’s migrant policy has come under fire with thousands protesting
The 17-year-old axeman was shot dead dead by police.
Authorities have said the refugee, who may have come from Afghanistan or Pakistan, had clear longer-term ties to Islamist extremist groups.
Last month a Syrian asylum seeker blew himself up in Ansbach outside a music festival killing himself and inuring 15 people.