A mid-ocean stand-off between Australia and Indonesia appeared to be developing as a customs vessel tried to return a boatload of rescued asylum seekers to a reluctant Indonesia.

Up to 56 asylum seekers were rescued from their wooden boat in Indonesia's search and rescue zone by an Australian ship on Thursday and, rather than taking them to Christmas Island, it is seeking to return them to Indonesia.

An Australian Customs patrol boat is trying to turn a boat with 56 suspected asylum seekers back to Indonesia within its search and rescue zone.

Conflicting reports are emerging about the asylum seekers from the Indonesian search and rescue agency, Basarnas, and the Australian Customs department has declined to comment. Immigration minister Scott Morrison's office released only a one-line statement late on Thursday saying:

"Australian authorities are liaising with their Indonesian counterparts in relation to a vessel that has requested assistance as the vessel is within Indonesia's Search and Rescue zone".