A federal judge on Tuesday threw out the government's case against a former Islamic charity leader and partially overturned the convictions of two others, ruling prosecutors failed to prove all the charges. The charity leader, Samir Al-Monla, was cleared of all charges and immediately released. The two others - Emadeddin Muntasser and Muhammed Mubayyid - remain in custody pending sentencing next week on the remaining counts. The three were convicted in January of duping the US government into awarding their Boston-based organization, Care International Inc., tax-exempt status by hiding its pro-jihad activities. Care International, which is now defunct, described its mission as helping war orphans, widows and refugees in Muslim nations. But prosecutors said the organization also distributed a newsletter promoting jihad and supported Muslim militants involved in armed conflicts around the world. US District Court Judge Dennis Saylor IV on Tuesday overturned conspiracy and tax-related convictions against Al-Monla and Muntasser, saying prosecutors did not prove the two conspired to lie to the Internal Revenue Service tax agency when the organization applied for tax-exempt status, defense attorney Charles P. McGinty said. The judge also dismissed Mubayyid's conviction on tax conspiracy. Saylor, however, let stand Muntasser's conviction of lying to federal officials and Mubayyid's convictions of making false statements to federal officials and filing false tax returns. US Attorney Michael Sullivan said prosecutors were evaluating the judge's oral ruling and were awaiting a written opinion, but anticipated they would appeal. Both Muntasser and Mubayyid remain in jail and the judge will consider bail applications Friday, defense attorneys said. Muntasser's attorneys said they would try to convince the judge that he had already served enough time behind bars. Federal sentencing guidelines set the maximum punishment at six months and Muntasser has already served nearly that since his January conviction, defense attorney Kathleen M. Sullivan said. Mubayyid's attorney, Michael C. Andrews, did not immediately return a call seeking comment after business hours. He told The Boston Globe that he was disappointed and that his client could face as much as five or six years in prison when he is sentenced. Muntasser was born in Libya and was the founder of Care International. Mubayyid was born in Lebanon and was the group's former treasurer. Al-Monla, the group's president from 1996 to 1998, was born in Kuwait and is a US citizen. Their charity group, which was not affiliated with the well-known global relief organization CARE International, raised $1.7 million in donations from 1993 to 2001. Prosecutors acknowledged Care did some legitimate charity work, but said the group concealed noncharitable activities from the government. Prosecutors said, among other things, the men didn't disclose that Care had ties to the Al-Kifah Refugee Center in New York, which was linked to the 1993 World Trade Center bombing.