In a joint statement, Temer said Brazil had prepared a plane to go picking up the Brazilian children and bring them home if the separated families are eager to reunite.
Temer said he told Pence that the issue was extremely sensitive to the Brazilian society and the government, and asked him to give special attention to it.
He also thanked Pence for his willingness to find a solution to the crisis.
"Our government is ready to collaborate in the transport of the Brazilian minors back to Brazil, naturally, if this is the wish of the families," said Temer.
According to Brazilian Ambassador to Washington Sergio Amaral, 51 Brazilian children are confirmed to have been separated from their parents, and this number could be higher.
On the issue of immigration, Pence sent a message about the tough stance of the United States.
"To the people of Central America, I have a message for you. Don't risk your lives or the lives of your children by trying to come to the United States on a road run by drug smugglers and human traffickers. If you can't come legally, don't come at all," he said.
The United States has received severe criticism over the child separation policy. Images of the cage-like shelters, with children having only tinfoil blankets to keep warm caused international uproar. The worldwide criticism eventually led US President Donald Trump to sign a decree to halt the separations.
However, family reunifications have been slow. There are still thousands of children separated from their parents.