The nurses were working in various hospitals in Libya.
The 44 were among 58 nurses who had reached Tunisia from Tripoli two days ago. Another batch of 43 nurses had reached the Tunisian border on Monday.Watch video: Indian nurses return home from Libya
Chief Minister Oommen Chandy had wrote to External Affairs Minister Sushma Swaraj on August 1 seeking the Centre's help in arranging flight for facilitating the return of the nurses.
Fighting between rival militias in Tripoli over the past three weeks and clashes between Islamists and army in the eastern city of Benghazi have prompted several countries to evacuate their nationals and diplomatic staff.
Last month, 46 nurses, who were held captive by ISIS militants in Iraq, returned home by a special Air India Flight here bringing an end to their about month-long trauma.