Shahrzad Mansour, 31, and Neda Mostafaei, 26, were sentenced to death in September for smuggling methamphetamine into Malaysia in December 2010. Defence lawyers are appealing the case.
The two Muslim nations both use the death penalty against drug traffickers.
But Iran's foreign ministry warned last week that executing the women would have a "negative effect" on bilateral ties, and called for them to be spared.
In a statement, Malaysia's Foreign Ministry said that while it valued relations with Iran it could not tolerate "illegal activities, which are detrimental to Malaysia's image and security".
More From This Section
"Malaysia assures Iran of the independence of the judiciary system... It is in this context that we hope for Iran to understand that any decision of our courts is carried out in accordance to the due processes of law," it added.
More than 200 Iranians are jailed in Malaysia, mostly for drug-related offenses, the statement said.
About half of the 200 have been convicted, with 70 either serving a life sentence or on death row, it added.
The court was told that drug traffickers had promised them a free trip to Malaysia in exchange for transporting "food items" that were filled with methamphetamine without their knowledge.
The Malaysian judge in the case dismissed that defense as a "fairy tale".
Though hundreds of people are on death row in Malaysia, the country has carried out few executions in recent years.
Iran has one of the world's highest execution rates, with more than 500 cases last year and almost the same number so far this year, according to human rights watchdogs.