national space agency is the upper hand organization for managing space activities and is under command of Surena Sattari the vice president for science and technology.
جزئیات ساختار جدید فضایی کشور/ 4 نهاد متولی هوافضا میشوند
Khamenei doesn't interfere in the details, it's not his duty.
Iran has a comprehensive national science map, government organizations have to act and plan according to this map, yet no enforcement policy has been predicted, they can simply dodge the framework and say we didn't reached the goals, the way Rohani's government did in the case of space program, in recent interview the head of space agency clearly said he doesn't care about the "sending human to space" program, and he easily dodged his responsibilities by saying there is no budget.
It's not the khamenei who defines the projects but government, it's not the khamenei who defines their budget, but government, it's not khamenei who defines launch dates but government.