The first part of a controversial series on the 11 September attacks was misrepresentative despite being re-edited, the Clinton Foundation says.
The two-part drama ties in with the fifth anniversary of the attacks
US network ABC "chose fiction over fact and entertainment over education" by misquoting Clinton administration officials in The Path to 9/11, it said.
The former president's aides were angry at suggestions he failed to deal with an Islamic militant threat before 2001.
ABC altered the drama, lasting two and a half hours, before transmission.
It declined to say whether any of the last-minute changes were made to address the complaints.
But parts of the production which drew the most fire from leading Democrats were toned down.
The Clinton Foundation - a charitable organisation set up by Mr Clinton - said ABC had received warnings "from members of the 9/11 Commission, 9/11 family members and public officials from across the political spectrum" about supposed inaccuracies.
"Their claims of edits notwithstanding, The Path to 9/11 had Clinton administration officials saying things they did not say and doing things they did not do," claimed spokesman Jay Carson in a statement.
"Many of these scenes are directly contradicted by the 9/11 Commission Report. The American public deserved better."
The foundation released a four-page document outlining three elements of the programme which it claimed were misrepresentative of real-life events.
Actress Shirley Douglas plays Madeleine Albright in the docu-drama
ABC was wrong to suggest the Clinton administration was "reluctant to kill" Osama Bin Laden, it said.
It was also unhappy at the suggestion President Clinton was "too preoccupied" with impeachment and the Monica Lewinsky affair to focus on terrorism - scenes which were re-edited before broadcast.
And it questioned the claim that former US Secretary of State Madeleine Albright "alerted the Pakistanis in advance of a 1998 US missile strike".
This scene, which indicated that the decision was a key factor in Bin Laden getting away, was left intact by editor.
The programme, broadcast in the US on Sunday evening, featured a disclaimer.
This was aired three times and emphasised that it was not a documentary.
The original version contained a note in the opening scenes that the film was "based on the 9/11 Commission report".
It said: "For dramatic and narrative purposes, the movie contains fictionalised scenes, composite and representative characters and dialogue, as well as time compression."
Thomas Kean, head of the commission that investigated the 9/11 attacks and a backer of the film, said on ABC's This Week Sunday that he had not seen the final cut of the movie but urged people to watch it.
"If people blame Bill Clinton after seeing this, then the mini-series has failed," said Mr Kean, the former Republican New Jersey governor.
"That's wrong and it shouldn't happen."
The first part of the mini-series, starring Harvey Keitel and Donnie Wahlberg, was screened to coincide with the fifth anniversary of the 11 September terrorist attacks.
The same version was also broadcast in the UK on BBC Two.