Mr Turnbull met with President Baron Waqa Friday on the sidelines of the Pacific Islands Forum in Micronesia.
The meeting between the pair follows a decision by the Nauruan Government to refuse a visa to crossbench MP Andrew Wilkie, who had planned to visit the immigration detention centre on the island.
Mr Turnbull used the meeting to thank President Waqa for his Government's support regarding the centre, which has been in use since it was reopened by the Gillard government in 2012.
"It's very, really, very much appreciated and saving many, many lives too. That is the critical thing."
According to the latest statistics from the Department of Immigration and Border Protection, 411 people were counted as living in the Nauruan centre.
The statistics, dated July 31, included 49 children.
Mr Wilkie was refused a visa on Tuesday, less than a week after Danish politicians were also blocked from accessing the island.
Greens Senator Sarah Hanson-Young was also denied a visa earlier this year, after being spied on while visiting the centre in 2013.
Mr Wilkie said the public had "a right to know what goes on" in the centre and took aim at the Turnbull Government for not supporting his attempted trip.
In an earlier statement, Mr Wilkie cited the reports surrounding the thousands of leaked files alleging abuse of children and adults in Nauru's offshore immigration centre.
The reports prompted a motion from Labor, whose motion to appoint an Independent Children's Advocate passed the Senate last week — 35 votes to 33.