Khamenei spoke after days of public spats between Rouhani's government and hardline opponents and as Tehran held what it called a "satisfactory" round of talks with visiting UN inspectors.
The disputes have focused mostly on a deal struck with world powers in November that has put temporary curbs on Iran's nuclear activities in exchange for modest sanctions relief and the return of billions of dollars in frozen Iranian assets.
"It has only been a few months since the government has taken the reign," Khamenei told commanders of Iran's air force in remarks reported by one of his websites, leader.Ir.