Border protection authorities have denied they're running a ''prison ship'' off the coast of Christmas Island for asylum seekers arriving in Australian territorial waters.

Immigration officials faced a grilling at a Senate estimates hearing on Monday night about unconfirmed reports an asylum seeker boat was intercepted off Christmas Island in mid-May and its passengers are in custody on the Customs Ocean Protector ship.

Senator Sarah Hanson-Young. Credit:Alex Ellinghausen

Customs chief executive Michael Pezzullo maintained that only an illegal foreign fishing boat had been intercepted near Christmas Island recently.

Australian Greens senator Sarah Hanson-Young referred to reports Christmas Islanders saw clothing packs being taken out to the Ocean Protector.