Two asylum seekers have drowned and another two are critically injured after their boat capsized in waters off Christmas Island.

The fishing boat was 15 nautical miles (27.7 kilometres) north of the island when it was struck by two waves this morning.

The boat overturned, throwing the 95 people on board into the water.

Home Affairs Minister Jason Clare says 93 survivors were plucked from the water by a Customs vessel.

He says a young boy aged around four or five died, along with a woman in her 30s.

Mr Clare says those injured are a child aged around six or seven and a pregnant woman in her 20s.

"[They are having] breathing difficulties from ingesting water and potentially some diesel that was on the surface of the water," he told a press conference.

The Royal Flying Doctor Service has sent a medical team to the Island to collect the injured and will fly them to Perth overnight.

The child will be treated at Princess Margaret Hospital and the woman will be taken to Royal Perth Hospital.

Mr Clare says border control vessel Ocean Protector had been tracking the boat since late last night after authorities received a distress call from someone on board.

He says Ocean Protector saw the boat around 3am (AEDT) today but it did not appear to be in distress.

Two Customs officials boarded the boat just before it overturned around 10am.

"The vessel stopped, and that allowed the Border Protection officers to... embark on the vessel," Mr Clare said.

"At that time two waves hit the boat. That caused the boat to roll over on its side and a number of individuals went into the water."

Christmas Island Administrator Jon Stanhope says the large group of survivors was transferred to the island by the Customs vessel.

"I can say at this stage, and I think it adds to the sadness and the sombre nature of an event such as this, that a significant number of those who've come ashore are children," he said.

The injured have been taken to hospital while the others will undergo health, security and identity checks.

Prime Minister Julia Gillard has told Channel Ten it is a dreadful tragedy.

"My message is a very clear one: do not pay a people smuggler, do not get on a boat," she said.

"If you take the chance then tragically too many people lose out on the way," she said.

Rear Admiral David Johnston says the nationalities of those on board are not yet known, but initial indications suggest they are from Afghanistan.

"There are men and women and some juveniles within the 95," he said.

"The numbers are still being confirmed but there are around 17 juveniles."

He says three Indonesians were among the 95 people on board.

"Whether they are crew or not is yet to be determined," he said.

Christmas Island Administrator Jon Stanhope said it was fortunate Customs officials had already detected the boat before it capsized.

"The Ocean Protector was approaching the scene at the time the boat capsized," he said.

"I think it's a very fortunate coincidence that Customs were within the vicinity and were able to respond very quickly."

Local police will investigate the cause of the capsize and present their report to the coroner.

Customs officials involved in the rescue efforts will be provided with counselling services.

'Dramatic increase' in boats

Customs officers stopped another boat with 128 people on board north of Christmas Island yesterday.

A boat carrying four passengers and two crew was also intercepted south-east of the Ashmore Islands yesterday.

Mr Stanhope says Government resources are clearly under pressure.

"Six or seven boats have come to Christmas Island," he said.

"I have no doubt the dramatic increase is putting a strain on the Department of Immigration, Serco, Customs and other offices here that are involved in the management of asylum seekers and the detention facilities."

Mr Clare says improving weather is having an impact.

"We're entering the end of the monsoon season and the weather conditions off the coast of Christmas Island have improved dramatically over the course of, I'm advised, the last nine to 10 days," he said.

"And as a result of that you're seeing an increase in the number of boats that are travelling to Christmas Island."

In December 2010, 50 people died when a boat carrying asylum seekers smashed into rocks off Christmas Island.