The Immigration Department said in a statement that the women were taken into the centre on Tuesday.
They had been on the bus with their husbands and the 10-year-old son of one of them since flying into Darwin from Nauru on Saturday night.
The brother-in-law of one of the women, Soliman Shirvani, told AAP he was relieved they were off the bus.
But he said he had not been able to speak to his family since Sunday night and did not know anything further about their condition.
He said the couples, who had been living in the Nauru community as recognised refugees, understood they would be housed in the Darwin community in the weeks leading up to the births, something the Department of Immigration has disputed.
One woman had experienced complications with her pregnancy, and Nauru lacks appropriate medical facilities, which is why they were transferred.
It is understood the 10-year-old boy left the bus on Monday afternoon and was accommodated in the facility at Wickham Point, about 40km south of Darwin.
Two International Health and Medical Services midwives had been monitoring the women overnight, Immigration and Border Protection Minister Scott Morrison said in a statement.
"The women and their families were temporarily transferred to Australia for medical purposes. The families hold valid Nauruan visas and have been settled in that country."
They held no Australian visa, he said.
"The women have been placed in the facility best suited to their medical needs. Other family members have been accommodated voluntarily, according to their preference," he said.
Ian Rintoul, spokesman for the Refugee Action Coalition, said the fact it took two and a half days to resolve the matter "says everything about the contempt the minister has for pregnant women who have come here as refugees".
He said it was yet to be revealed what the terms of the agreement were.
"A bus was not an appropriate place for them to be kept," he said.
"They should not be in immigration detention, they deserve respect as people found to be refugees. They should not be deprived of their liberty."
