Surrey had feared that they would lose the services of the off-spinner during the three limited-overs internationals that are due to take place between 12-19 June.
But the Pakistan Cricket Board have agreed to let Saqlain and Middlesex all-rounder Abdur Razzaq stay with their counties.
"The Board had given permission to me and Razzaq, who will play for Middlesex," Saqlain said.
"But I am not sure when we will be required to play for Pakistan this year again."
Pakistan are also scheduled to take part in a triangular tournament in Morocco in August and the ICC Challenge Cup in Sri Lanka a month later.
Surrey have signed Pakistan all-rounder Azhar Mahmood to cover for Saqlain's absence on international duty.
Saqlain will return to the club earlier than expected after New Zealand's tour of Pakistan was cut short following a bomb blast outside the tourists' hotel in Karachi.
And New Zealand Cricket chief executive Martin Sneddon raised doubts about future tours to Pakistan.
"We probably have to let the dust settle before we make any hard-and-fast decisions," he said.
"But it's fair to say the situation regarding Pakistan becomes a bit different after the scenes in Karachi.
"As far as the greater region is concerned, I think it's too soon to be drawing any conclusions. I'm reluctant to speculate on what might happen in other countries such as India and Sri Lanka."