The programme, Faith, Hate and Charity, broadcast on Sunday, alleged that the charity donated thousands of pounds to voluntary organisations on Israel's West Bank that support the party and help to spread its ideology.
Although Hamas won the Palestinian elections, it is widely condemned and boycotted for its support of suicide bombings.
The Charity Commission cleared the charity of misapplication of funds after official inquiries in 1996 and 2003.
But Kenneth Dibble, executive director of legal and charity services at the commission, admitted on the programme that the most recent investigation "had not been in-depth".
Ibrahim Hewitt, chair of Interpal, said the programme was "a wholly unbalanced and incomplete picture". He said Interpal was a politically neutral organisation and had never supported terrorism.