The source said: "Ibrahim Mohamed Ahmed, a senior intelligence officer who was in charge of the airport died along with two others. He had many enemies because of his work. We can't point a finger now, but certainly it's his enemies who are behind this."
There has been relative calm in Mogadishu since the interim government and its Ethiopian military allies declared victory over anti-government fighters two weeks ago, in a move that has encouraged small numbers of Somalis to return home.
More than half of the city's one million people have been forced to flee their homes because of clashes between allied Somali-Ethiopian troops and fighters which have killed at least 1,300 people in the city's worst fighting in 16 years.
Holmes, the highest ranking UN official to visit Somalia since the recent fighting, hopes to push the government to allow relief agencies full access to the country's population.
Holmes said: "There is a serious humanitarian crisis and I want to come and see for myself, to talk to the authorities, to try to pressure them on the need to do all they can to facilitate humanitarian aid.
"It is their responsibility to look after civilians, to protect civilians and at the very least not to obstruct aid."
Holmes at first considered scrapping his tour of Mogadishu, but later went on to visit a cholera treatment centre and then the Villa Somalia presidential palace where he had a private meeting with Yusuf.
Earlier, women and children waved and yelled from the doorways of buildings pockmarked with bullet holes as his convoy rolled through Mogadishu streets lined with African Union (AU) troops.
Last month the UN accused all sides in the Somalia conflict of breaking humanitarian law by indiscriminately firing on civilian areas in Mogadishu.
Aid workers have also complained that Somali authorities had failed to clear food shipments for distribution and said they were being harassed at checkpoints.
Since then, the government has promised to clear obstacles in providing aid to tens of thousands of people.
In recent weeks, it has ordered civilians to be disarmed, deployed troops to flush out fighters from rebel areas and allowed security forces to seize Muslim women's veils to stop fighters from disguising themselves for attacks.
Holmes said the situation must become more stable before more AU peacekeepers could be expect in Somalia to boost a 1,500-strong Ugandan contingent stationed there.
The AU has appealed to member states who have pledged troops to deploy them quickly to allow Ethiopian troops to withdraw.