Colonel Abdikadir Adan Shire, also known as Barre Hiraale, the leader of the Juba Valley Alliance, a clan-based militia that controls the area, was reported to have fled the city on Sunday, officials and eye-witness in Kismayo said.
Barre Hiraale's hasty departure from the city followed a split within the alliance on how to respond to advance of the Islamic Courts Union (ICU), which seized Mogadishu and other parts of southern Somalia earlier this year, Yusuf Mire Mahmud, his deputy said.
"I wanted to talk to the ICU, and he did not. He sent a delegation to Ethiopia and that was the final straw for me," Mahmud told Reuters.
The departure of Barre Hiraale has opened the way for the peaceful advance of the Islamic militia into the city, Mahmud said.
"Tomorrow the people of Kismayo will welcome the courts," he said, adding that Islamist forces were some 100 km away.
Kismayo is the largest port in southern Somalia and is 500 km (300 miles) south of Mogadishu, the country's capital.
Islamist plan advance
An Islamist source in Mogadishu said troops were ready to enter the city "at the invitation of the people".
"We'll go in either late tonight or tomorrow morning," the source told Reuters.
The Islamic Courts Union have urged Barre Hiraale, who is also defence minister in the interim government, to hand over the town, pointing out that many of the militias protecting it have clan alignments close to those of the Islamists'.
Kismayo is the largest port in southern Somalia
On Saturday, inhabitants of villages south of Mogadishu described seeing several hundred Islamist fighters traveling towards Kismayo, traveling in heavily-armed pick-ups known as 'battlewagons' or 'technicals'.
"I saw 30 battlewagons passing by and headed to Kismayo," said Ali Nuur Jiisow, a resident of Afgoi Yerey village on the road between Mogadishu and the port-city.
In the past few months, the Islamic Courts Union has expanded rapidly from beyond its base in Mogadishu to take over large areas of Somalia.
Their advance has largely been at the expense of Somalia's largely-powerless interim government which is backed by Ethiopia and recognized by the United Nations and most foreign governments.
The interim government was formed in 2004 in an attempt to end the civil war that has divided the country since rival warlords ousted dictator Mohammad Siad Barre in 1991.
Abdirahman Dinari, the interim government's spokesman, said any attack on Kismayo would breach a ceasefire deal recently signed between the government and the Islamists in Khartoum.
"We're requesting that the international community pressurise the ICU to stop attacking," Dinari said from the government's temporary base in Baidoa, near the Ethiopian border.
Thousands of Kismayo's inhabitants, fearing heavy fighting between the Islamists and the Juba Valley Alliance, have fled to Kenya in recent days, with 300-600 refugees arriving daily in the Dadaab camps just over the border, according to the UN.