The government of the No.2 oil producer in Africa has faced a storm of criticism after some international media reported it had "banned Islam", causing embarrassment for this member of the OPEC oil cartel dominated by Muslim states.
The outcry followed an announcement by the Ministry of Justice earlier this month listing 194 "religious confessions" whose requests for registration it rejected, among them the Islamic Community of Angola (COIA).
Requests from a number of evangelical Christian and other non-Muslim groups were also turned down.
A COIA leader, David Ja, told Reuters the authorities had closed dozens of mosques and even demolished some across Angola's 18 provinces, in what he called a targeted crackdown in the predominantly Catholic former Portuguese colony.
In a briefing to diplomats on Friday, Foreign Minister Georges Chikoti said there had been "misunderstandings" about the government action.
"There has been no Muslim persecuted," Chikoti said.
"There is no government policy to persecute one church or religion, that was an interpretation made by the Islamic community in Angola," he said.
Chikoti said Angola's constitution defends the right to religious freedom, but the law requires religious groups to meet legal criteria to be recognized as official churches.
"There are eight Islamic denominations here, all of which requested registration. But none fulfilled legal requisites so they can't practice their faith until concluding the process."
He said some groups had not registered their mosques as official places of worship but did not go into further detail on what legal requirements they had not met.
Organisations need to have more than 100,000 adult members and have a presence in over two thirds of the country's territory to be considered legal entities.
Most of the estimated 18 million Angolans are Catholic, a legacy of Portuguese colonial rule which ended in 1975.
MUSLIM LEADER SEES "SUBTERFUGE"
Ja said the around 900,000 Muslims in the country were feeling persecuted and called the government's argument over legal requirements "a subterfuge to ban Islam".
He said his organization had enough members and covered enough territory to quality for registration. "It is a way to ban a religion they think threatens Angolan culture," he added.
Many Muslims settled in Angola after arriving from West African countries after 1992, when President Jose Eduardo dos Santos' MPLA government abandoned Marxism. Many fled political persecution at home, others came to work in diamond fields in eastern Angola.
Chikoti said Angola faced a big influx of illegal immigrants and many of these were Muslims.
He added many Muslims obtained licenses to build commercial warehouses and then used the sites to build mosques, without obtaining legal permission or building licenses specifically for such places of religious worship.
"None of the mosques were built in accordance with the law ... In Angola there is a big number of Muslims who enter the country illegally and then practice their faith in their places of commerce," he said.
Alex Vines, an Angola expert at London-based think-tank Chatham House, said the issue had been clumsily handled by the government and the recent media headlines about a "ban on Islam" could attract hostility from radical Islamist groups.
"It might not only radicalize Muslim communities in Angola but could make it a target for jihadists," he said, adding that it could also affect Angola's commercial ties with Muslim nations, such as Turkey, Indonesia and Gulf states.
(Reporting by Shrikesh Laxmidas; Editing by Pascal Fletcher and Andrew Heavens)