Sheikh Hassan Dahir Aweys, leader of the Islamic Courts Union, also told all Somalis to take up arms against Ethiopian troops assisting the Somali government.
"We have been asking the Ethiopians to leave our country for a long time," Aweys told thousands at the Isbahaysiga mosque in Mogadishu, the Somali capital, in a speech to mark the end of the Muslim holy month of Ramadan on Monday.
"This is the end of that request.
"We are now telling them that from now on, their graves will be littered everywhere in Somalia. We are not going to tell the world that Ethiopia is interfering in Somali affairs any more.
"We will now start fighting. I am calling on all Somalis wherever they are to start jihad against the invaders and those who support them."
Tensions between Ethiopia, which backs Somalia's weak but internationally recognised government, and the Islamists, who control much of the south of the country, have been mounting in recent months.
Islamist fighters now control much of southern Somalia
Another senior member of the Islamic Courts Union, Sheikh Sharif Sheikh Ahmed, said:
"We urge Ethiopian people, who are not part of this aggression against Somalia, to revolt against and remove the oppressive regime led by [Ethiopia Prime Minister] Meles Zenawi."
In other towns, Somalia's Islamic leaders made similar calls, saying they would to drive Ethiopian forces from Baidoa, the only town the Somali government controls, about 250km northwest of Mogadishu.
Ethiopia, with almost half of its 77 million population Muslim, is fearful that a victory by the Islamic Courts Union will strengthen Somalia as a regional power and destabilise the region.
Addis Ababa has consistently denied that its forces are in Somalia, but on Thursday Meles acknowledged that his troops were training Somali government forces.
Since June, the Islamists forces have taken over much of the south and centre of the east African country, defeating a coalition of local commanders who largely worked with the Somali interim government based in Baidoa.
Muslims make up nearly half of
the Ethiopian population
The Ethiopian government has said that it will respond to any attack on the government in Baidoa and that it would also take firm action against any attempt to radicalise its own Muslim population.
"We will defend the [Ethiopian] government if attacked by the jihadists," Bereket Simon, a minister without portfolio in the Ethiopian government and a key ally of the prime minister, said.
"If they try to overthrow the legitimate government, we will help the government."
By Monday, the Islamists had also reversed one of the Somali government's few recent military successes, by recapturing the town of Burhakaba which government troops had seized last week.
Sheikh Mohamed Ibrahim Bilal, a commander allied to the Islamists, said: "The town is in the hands of the Islamic courts militia."
"The government forces escaped before we arrived," Bilal told AFP from Burhakaba, which is about 60km southeast of Baidoa.
However, government commanders said their troops had left the town without coming under attack.
"I am calling on all Somalis wherever they are to start jihad against the invaders"
Sheikh Hassan Dahir Aweys,
Islamic Courts Union leader
"We moved away from Burhakaba because we managed to restore security," Said Hirsi Dhere, a government commander who had initially captured the town, told AFP .
On Sunday, at least five people were killed in clashes between a pro-government forces and Islamist fighters near the town of Buale in southern Somalia, the latest in such fighting.
The fresh violence has sent tensions soaring in the region, with tens of thousands of Somalis fleeing into neighbouring Kenya to escape.