Deputy Foreign Minister Hassan Ghashghavi said Malaysia should spare the women "so that the friendship and brotherhood" between the two countries can continue.
The two women, Shahrzad Mansour and Neda Mostafaei, were sentenced to death in December 2010 after being convicted of smuggling methamphetamine into Malaysia.
An Iranian official said unknown drug traffickers tricked the women into unknowingly taking bags containing the drugs into Kuala Lumpur.
Iran itself has one of the highest execution rates in the world and frequently executes drug traffickers, as well as those convicted of violent crimes such as murder, rape, and armed robbery.
Convicted adulterers are also sometimes executed.