The Yemen Interior minister uncovered what it said was a spy ring led by former members of the Iranian military, the BBC reports.
Yemeni forces in August 2009 launched a campaign against Houthi rebels in northern Yemen. The conflict threatened to spill into Saudi Arabia before the Yemeni government reached a cease-fire. Iran at the time was suspected of meddling in Yemeni affairs by supporting the rebels.
Hadi told the county's War College in Sanaa that Iran should stay out of Yemen's internal affairs.
"We hope that our Iranian brothers don't interfere in Yemen's affairs and to take into account the critical circumstances Yemen is undergoing," Hadi was quoted by the official Saba news agency as saying. "I tell you all, from the War College, leave Yemen alone and it is enough."
Yemen is in the midst of a political transition period following February elections. Long-time President Ali Abdullah Saleh stepped down last year after his country was caught up in the so-called Arab Spring. Terror attacks attributed to al-Qaida have increased since Hadi took power.