Jama Ali Jama was driven from the regional capital Garowe earlier this week by forces loyal to former Puntland leader, Colonel Abdullahi Yusuf Ahmed
He told the BBC's Focus on Africa programme he had not fled for his life, but was now organising the logistics of retaking Garowe from Puntland's commercial capital, Bossasso.
Correspondents say more than half the population of Garowe, mostly women and children, had now fled the city.
Aggression
Clan elders elected Jama Ali Jama as the new head of Puntland earlier this month, but his appointment was immediately rejected by Abdullahi Yusuf, who described the vote as futile and illegal.
Mr Jama was insistent that he had the support of the people of Garowe, who he said were mobilising against Colonel Abdullahi's forces.
"The people of Garowe are organising themselves and we are trying to send them some assistance. I'm sure the people will capture it," he said.
"We appeal to all the people of Puntland to resist this aggression," he said.
Mr Jama said he believed at least 20 people had died in recent fighting.
The BBC's Hassan Barise said mainly women and children were fleeing Garowe for fear of further fighting as Colonel Abdullahi mobilised militia to consolidate his hold on the city.
Ethiopia troops
The AFP news agency reported, meanwhile, that 1,000 heavily armed Ethiopian soldiers had entered Puntland at the invitation of Colonel Abdullahi.
The report quoted unidentified witnesses as saying the troops were backed by heavily equipped armoured vehicles and pick-up trucks mounted with heavy machine guns.
But Yemane Kidane, Chief of the Cabinet at Ethiopia's Ministry of Foreign Affairs, described the report as "totally unfounded".
"It is our policy that no Ethiopian soldiers crosses into Somalia," he told the BBC.
"I can tell you for a fact that not a single Ethiopian soldier is inside Puntland or Somalia," he said.
It is no secret that there has been a build-up of Ethiopian forces along the country's border with Somalia.
But Mr Kidane said that all Ethiopia wanted was to see Puntland elders resolve their problems for the sake of peace and stability in the region.
Puntland was created in 1998, partly to avoid the violence that has plagued Somalia which had been without a central government since 1991.