Isik also told a news conference that NATO countries have not presented a "financially effective" offer on an alternative defense system. NATO member Turkey in 2015 canceled a $3.4 billion tender for a long-range missile defense system that had been provisionally awarded to China.
Turkey then said it would consider developing a missile system locally, but that stance later shifted.
"It is clear that Turkey needs a missile defense system but NATO member countries have not presented on offer which is financially effective," Isik told a news conference.
"Work on the S-400 has reached a final point. But the final stage does not mean 'let's sign a deal tomorrow morning'".
He said Turkey would not be able to integrate the S-400 into the NATO system.