The 31-year-old full-back completed his medical in Istanbul on Wednesday.
No details were given of the deal but according to Italian press reports the Turkish club have an option to buy Nagatomo for seven million euros ($8.6 million).
Nagatomo, who joined Inter in January 2011 and has made 210 appearances scoring 11 goals, is hoping for more playing time ahead of the World Cup in Russia.
The former FC Tokyo player — capped 101 times by Japan — has played in just one of Inter’s last 10 league games.
He was also part of the side which won the Italian Cup in the 2010-11 season.
