He said the fact that one of those kidnapped was a Chinese national could complicate the situation further following the disappearance of MH370, which had mostly Chinese nationals on board.
"There may be those who are attempting to drive a wedge between China and us. They may be trying to take advantage of the situation," Najib said after a bilateral meeting with his Australian counterpart Tony Abbott at the Commonwealth Parliamentary Office here.
Najib, however, believes ties with China will remain strong despite the kidnap incident.
Najib said Malaysia had sought the cooperation of Filipino authorities on the matter, while police were investigating how the incident could have happened.
A news portal had reported that rebel group Abu Sayyaf was responsible for the abduction.
Filipino military sources told Rappler.com that the two women were taken by six former Moro National Liberation Front (MNLF) members who had joined Abu Sayyaf.
In Kota Kinabalu, Sabah Chief Minister Datuk Seri Musa Aman has ordered that all available resources be directed towards solving the kidnapping case at a resort in Semporna.
He said the Eastern Sabah Security Command (Esscom) director-general Datuk Mohammad Mentek had briefed him on the kidnapping.