He was charged with smuggling country information, sedition, treason, and blasphemy in 2003, and a case was filed against him on 24 January 2004 by Mohammad Abdul Hanif, head of Airport Police Station of Dhaka, who claimed that he was a Mossad agent based on the documents found in his possession.

[9] Choudhury faced charges of smuggling information out of country, money fraud,[10] sedition, treason, blasphemy, and espionage since January 2004 for attempting to attend a conference of the Hebrew Writers' Association in Tel Aviv.

[15] According to Bret Stephens, a columnist for The Wall Street Journal, in September of the same year, despite the government's reluctance to prosecute, a judge with Islamist connections ordered the case to continue because Choudhury had "spoil[ed] the image of Bangladesh" and "hurt the sentiments of Muslims" by lauding Jews and Christians.

[citation needed][12] Choudhury later lodged a case in the Court of Metropolitan Magistrate against his attackers, most of whom were affiliated with the Cultural Wing of the Bangladesh Nationalist Party (BNP).

[20] n March 2011, Aryeh Yosef Gallin, the founder and president of the Root and Branch Association (a nonprofit group that promotes cooperation between Israel and other nations), expelled Choudhury from its Islam-Israel Fellowship after reports accused the Bangladeshi of swindling "emotionally vulnerable single Jewish ladies" out of tens of thousands of dollars.

[1] On 7 November 2012, the Dhaka court sent Choudhury to jail in connection to an embezzlement case filed by his business partner Sajjad Hossain, chairman of Bangladesh Center for International Studies.