The Spanish club are due around €3 million from the transfer, with the payment originally scheduled for April 30. Fenerbahçe failed to meet that deadline, prompting Sevilla to take the matter to FIFA.
The governing body has now demanded payment of the overdue amount and has reportedly also ordered Fenerbahçe to bring forward the next instalment, which had originally been due at the end of October.
Fenerbahçe have confirmed they will comply with the order.
The Turkish club said in an official statement that it would make the payment on Monday, the first working day, before completing the necessary procedures to have a transfer ban lifted.
The dispute has already resulted in Fenerbahçe being temporarily prohibited from making transfers for three windows following Sevilla's complaint over the missed April payment.
En-Nesyri joined Fenerbahçe in a deal worth almost €20m, with the agreement allowing the Turkish club to spread the payments over four years.
For Sevilla, the FIFA intervention provides an opportunity to recover another significant portion of the outstanding transfer fee.