BERLIN (Reuters) - Germany's interior minister has dismissed the head of the Federal Office for Migration and Refugees (BAMF), which is mired in a scandal over irregularities in making asylum decisions, a spokesman said on Friday.

The decision by Horst Seehofer, leader of the Bavaria-based Christian Social Union (CSU), comes at the height of dispute over immigration that threatens to splinter Chancellor Angela Merkel's conservative bloc.

Merkel's Christian Democrats (CDU) and CSU sister party are at odds over how to tackle the issue of migrants, which is also causing strain among members of the European Union.

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BAMF chief Jutta Cordt had come under criticism after an internal review by BAMF of 4,568 asylum rulings had found that the Bremen branch knowingly and regularly disregarded legal regulations and internal rules.

The Interior Ministry spokesman said Seehofer had informed Cordt on Wednesday of his decision to dismiss her.

A replacement for the head of BAMF, which is overseen by the ministry, will be announced soon, he added. The BAMF press office could not be reached for comment.

The decision was first reported by Spiegel magazine.

The dispute between the CSU and CDU threatens the future of Merkel's government three months after it took office in a coalition with the centre-left Social Democrats (SPD).

Merkel wants to find a European solution to the migration issue in the two weeks ahead of a June 28-29 EU summit. But the CSU does not want to wait and is urging Germany to take unilateral action.

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Seehofer, whose party faces an election in Bavaria in October, wants Germany to refuse entry to migrants who have already registered in countries further south, a plan that Merkel opposes.

As a compromise, the CDU proposes turning away at the border migrants who have already applied for asylum and been rejected. The CDU also suggests forging bilateral deals to make it possible to send back people who have already applied for asylum in another EU country.