BERLIN, July 1 (Reuters) - Chancellor Angela Merkel said on Sunday she wants her Christian Democratic Union and its Bavarian allies to continue working together.

A dispute over how to handle migration has plunged Merkel's three-month-old "grand coalition" into crisis and weakened the conservative leader, forcing Merkel to scramble to try to reach deals with individual EU members.

Facing regional elections in October, the Christian Social Union (CSU), the sister party of Merkel's Christian Democrats (CDU) has been pushing for tougher rules on migration.

"I share the CSU's aim of on the one hand reducing the number of immigrants being brought to Europe by smugglers, and on the other hand I also share the view that asylum seekers can't simply choose which country they want to go to," Merkel said in an interview with German broadcaster ZDF, emphasising her willingness to work together with the CSU.

Differences with the CSU only pertained to the way how to achieve a reduction in migration, not to the goal as such, Merkel said. (Reporting by Thomas Escritt and Andreas Rinke Writing by Andreas Cremer Editing by Victoria Bryan)