Yemen's Foreign Minister Abubakr al-Qirbi told al-Mithaq newspaper he had summoned the Iranian ambassador.
"We expressed our position to the Iranian ambassador in Sanaa. We warned them that the media rhetoric does not serve bilateral interests between us and Iran," he was quoted as saying in the paper, owned by Yemen's ruling party.
"If Iranian media want to be a tool in the hands of the subversives in Saada and to adopt their positions, this will have negative consequences for Yemeni-Iranian relations, which will require us to take difficult decisions."
Yemen said this month the rebels were receiving financial support from abroad, but did not name Iran.
The rebels of the Shi'ite Zaydi sect — which follows a different version of Shi'ite Islam to that practiced in Iran — have said they were bombed by Saudi jets. Saudi Arabia has become a key ally of Yemeni President Ali Abdullah Saleh.
Saudi-owned Arab media have accused Iran of funding the rebels since the fighting first broke out in 2004.
An Iranian foreign ministry spokesman last week denied Iranian involvement and called for a political solution.
Yemeni officials say the rebels want to restore a Shi'ite state overthrown in the 1960s.
The rebels say they want more autonomy, including Zaydi schools in their area. They oppose the spread of Saudi-influenced Sunni fundamentalism and say they are defending their villages against government oppression.
More than 100,000 people, many of them children, have fled their homes during the recent surge in fighting, a U.N. agency said this month, and aid groups have complained of poor access to the war zone, which has been closed to media.
Yemen is also battling al Qaeda militants and secessionist discontent in the south.
An assassination attempt on Saudi Arabia's deputy interior minister last week fed Western and Saudi fears of Yemen becoming a launchpad for a new round of al Qaeda attacks in the region. The attacker entered Saudi Arabia from Yemen.
(Writing by Andrew Hammond; editing by Andrew Roche)
