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According to the newspaper Daily Times, the suspects have been shifted to Islamabad for interrogation.
There are, however, contradictory reports regarding the arrest of Moosa -- also known as Abu Moosa -- and his two aides.
Some sources claimed that Moosa was detained along with two others, including one Kifayatullah and Taliban leader Mullah Abdul Ghani Baradar.
Pakistani intelligence officials had recently informed the government about the presence of three Al Qaeda men residing in a bungalow in Gulshan-e-Iqbal and identified them as Rafique, Iqbal and Shakoor.
The sources said six others, including five foreigners, had also been arrested from different parts of the city. Four were arrested in Baldia Town and two Afghans in Nooriabad.
Communications intercepted by US authorities played a key role in tracking and arresting the suspects, who were in Karachi buying bomb-making equipment, the officials said.