The referendum on independence from PNG was to be held from October 12 but the Bougainville Referendum Commission had asked for an extension to ensure the electoral roll is in order.
The National newspaper reported Marape saying he had given his approval and his government intended to stick to the new deadline.
No announcement has been made on when the deadline will be.
Early next month the Joint Supervisory Board, which governs the relationship between the two governments, is set to hold a meeting in Buin, in south Bougainville.
Marape will attend and says he would campaign for a united PNG while there. Marape said his government was very sensitive to the issues that Bougainvilleans had gone through.
"We have deliberately kept silent because we don't want to be seen to be in their face trying to influence the outcome of the referendum," he said.