Jamil al-Majdalawi, a PFLP leader, said: "We informed the brothers in Hamas that regrettably we are not going to participate in the government because the political programme did not include a fundamental point for us - that the PLO is the sole, legitimate representative of the Palestinian people,"
Speaking to Aljazeera from Gaza, al-Majdalawi added that the groups had "achieved progress in some of the forms and we have given concessions about some points, in an attempt to find common denominators".
He said dialogue between the groups would continue.
"We will stand by Hamas to keep on its resistance", he added.
The PFLP became the last Palestinian faction to turn down Hamas's offer to form a coalition government.
Hamas defeated the long-dominant Fatah movement in a January 25 parliamentary election.
Hamas planned to present its cabinet to Mahmoud Abbas, the Palestinian president, later in the day.
Abbas, who has urged Hamas to accept the Palestine Liberation Organisation's interim peace accords with Israel, said he would not reject the cabinet, and expected parliament to convene soon for a vote of confidence.
Hamas's failure to attract any partners and its step to appoint Hamas loyalists to top ministerial posts could support US and Israeli efforts to isolate the new government.
"We are not going to participate in the government because the [programme] did not include a fundamental point - that the PLO is the sole, legitimate representative of the Palestinian people"
Al-Majdalawi said the PFLP's rejection of Hamas's offer should not be seen as a change in his group's opposition to all the agreements that the PLO had signed with Israel.
In a West Bank prison raid on Tuesday, Israeli forces seized PFLP leader Ahmed Saadat and other members of the group accused of involvement in the 2001 killing of an Israeli cabinet minister.