"The attacks against Afghanistan are unacceptable and we have condemned them. It is our clear position," Sheikh Hamad bin-Jassem bin-Jabr al-Thani said.
He was speaking to reporters here after a meeting between Qatar's emir, Sheik Hamad bin Khalifa al-Thani, and Iranian President Mohammed Khatami.
"What is happening in Afghanistan concerns the Islamic world, and we think that the culprits of the September 11 attacks, no matter who they are, should be tried justly. We think that the Afghan people should not be the victims of these attacks," the foreign minister said.
On October 8, the day after the air strikes began in retaliation for the September 11 terror attacks on New York and Washington, the emir said that he regretted them.
"We wish it hadn't come to this," he said after talks in Paris with French President Jacques Chirac. "We are in principle opposed to wars, opposed to seeing more victims falling."
Two days later, the foreign minister said Qatar would not let the United States use its airport facilities for its military operation against Afghanistan.
Qatar currently heads the 57-member Organization of the Islamic Conference (OIC), after succeeding heavyweight Iran last year. Next month it hosts a key ministerial meeting of the World Trade Organisation.
The emir and his foreign minister were in Tehran for talks on the Afghan crisis as well as regional issues.
Speaking just ahead of the Qatari delegation's departure, the minister said the two sides had talked over the Afghan "without discussing the future of that country, because it is up to the Afghan people to decide" their fate.
"For Afghanistan, we do not have precise plans and we think that it is unnecessary to call for a summit of the Organisation of the Islamic Conference," he added.
The emir and his delegation had been welcomed at Tehran's Mehrabad airport earlier Tuesay by Iranian Vice President Mohammed Ali Abtahi and Energy Minister Habibollah Bitaraf before heading to the Saad-Abad presidential palace, where they met with President Mohammad Khatami.
State radio said Khatami and the Qatari emir would discuss "bilateral ties, the Afghan crisis and regional issues."
On Sunday, Qatar, as head of the OIC, called for an urgent meeting of the United Nations Security Council to put an end to "Israel's aggressions" against the Palestinians.
Since the assassination of an Israeli cabinet minister last week by a radical Palestinian group, the Israeli army has re-occupied part of autonomous Palestinian cities in the West Bank, killing at least 25 Palestinians.
The 57-member OIC, based in the Saudi city of Jeddah, has condemned the September 11 attacks on the United States, but did not declare any official position toward the US-led strikes on Afghanistan, aimed at chief terror suspect Osama bin Laden and the Taliban regime which is sheltering him.
Tehran, for its part, has condemned both the September 11 attacks and the strikes on neighbouring Afghanistan, calling on the United Nations to lead the campaign against terror instead.
Meanwhile, in Doha, officials said the emir would visit Riyadh on Sunday for talks on the Afghan and Palestinian crises.
The London-based Al-Hayat daily said Tuesday the visit was decided after a telephone conversation between Sheikh Hamad and Saudi Crown Prince Abdallah bin Abdel Aziz, following a deterioration of the situation in the Palestinian territories.