Although details of Naykeya's move to Masr remain scanty, Nyakeya is said to have landed in Cairo to complete the transfer the capital-based side on Monday.
FC Masr were promoted to the Egyptian Premier League at the end of last season.
Earlier rumours suggested the former Gor Mahia youth player was set to join either Gor Mahia or newly-promoted Wazito.
Nyakeya was the fourth-most prolific striker at the end of the 2018/19 season after Enosh Ochieng, Allan Wanga, and Umaru Kasumba. He scored 14 goals.
Omondi takes Alex Mwangi's place and his arrival comes after the club hired Zedekiah Otieno as the new coach, and are also expected to fill the vacant assistant coach's position which was left by Sammy Omollo.