More than 50 asylum seekers who arrived on a boat on Monday night are still being held in Darwin, and some show signs of torture – breaching transfer policy

Asylum seekers who arrived on a boat into Darwin Harbour on Monday night are still being held in detention due to delays in medical clearances, and some show signs of having been tortured, Guardian Australia has learned.

It was believed that the transfer of the asylum seekers to Christmas Island had begun today, but according to Darwin Asylum Seeker Support and Advocacy Network (Dassan), they are still being held in Darwin facilities.

Guardian Australia has been told by a secondary source that the asylum seekers are being held in the Northern immigration detention centre, and two family-like groups are being held at Darwin airport lodge. It was previously thought that all asylum seekers were being held at Blaydin alternative place of detention.

According to the same source, there are 50 “Yemeni people from Somalia,” many with “visible signs of torture”, and four people from Pakistan. It is not know what is causing the delays in medical clearance of the asylum seekers. Other sources have since confirmed the nationalities and the claims of torture. According to one detention insider: “When you get refugees from Somalia, signs of torture and trauma go hand in hand.”

Current policy dictates that asylum seekers would normally be transferred within 48 hours.

A source “inside detention” told Dassan the boat had been intercepted at sea by an Australian customs vessel, and personnel handed over a note telling them to go back or they would be sent to Papua New Guinea. The customs vessel then left. The source told Dassan that passengers were scared, believing they had been abandoned, until the customs vessel returned a number of hours later.

It is not known what state the asylum seekers’ boat was in.

The immigration minister, Scott Morrison, on Friday confirmed the arrival and that notes are handed to asylum seeker vessels by customs.

“Of course I’m aware of what we do, we make sure people understand what our policies are whether that is at sea, whether that’s in Indonesia, whether that’s in Malaysia, whether that’s in Pakistan or Iran or any of these places, we make sure anyone who is seeking to come illegally to Australia by boat knows that it’s a vain effort,” he said.

The arrival of the vessel was confirmed on Tuesday, and it was believed there were children among the passengers.

When asked at the weekly press briefing on Friday about the delays in medical clearances preventing the transfer of these asylum seekers, Lieutenant General Angus Campbell said: “Those people and those people who arrived on Christmas Island immediately enter into the 48-hour rapid transfer process. There may well be some who don’t complete that process in 24 hours, but the great majority do.”

Calls throughout the week to Morrison have gone unreturned. A request for information or confirmation of these new details before the press briefing also went unanswered.

On the first day of the new parliament Morrison refused to answer questions put to him by the opposition on the Darwin arrival, citing operational reasons.

"This government is not running a shipping news service for people smugglers," Morrison said.

"As promised, we are running a military-led border security operation."

After reports in the Indonesian newspaper the Jakarta Post that four of six attempts by Australian authorities to turn boats around to Indonesia have been refused, Morrison was forced to concede that this was the case for two boats.

Last week Australian and Indonesian authorities were involved in a standoff over a boat carrying 56 passengers which got into distress in Indonesian waters. Indonesia refused the boat passage and Australian authorities had to take the passengers to Christmas Island.