The coffin of Naji, also known as Kamal Medhat, and the other three victims, draped in Palestinian flags, were carried about three kilometres through the streets of Beirut, the Lebanese capital, from Imam Ali mosque to the Palestinian "martyrs cemetery".
PLO guards marched in front of the thousands-strong procession chanting revolutionary songs, while some in the cortege carried photographs of the four victims and others waved Palestinian, Fatah and Hamas flags.
During Wednesday's procession, the PLO representative in Lebanon, Abbas Zaki, walked side by side with Hamas officials, including Osama Hamdan.
The Palestinian people fear Naji's assassination may further deepen the division of the factions.
"The Palestinian people are scared of internal strife and that foreign hands are encouraging this," Mhamad Shammal a Palestinian refugee told Al Jazeera.
The fear, however, was ruled out by Zaki.
"I am satisfied with the investigation process and we have the ability to catch the perpetrators and I am sure there won't be strife amongst Palestinians," he said.
Medhat was leading efforts to end the rift between Fatah and Hamas as well as several other Islamist groups operating in some of the 12 camps housing Palestinian refugees in Lebanon.
Medhat, in his 50s, was also a former aide to Yasser Arafat, the late Palestinian president, and a former intelligence chief for Fatah in Lebanon.
Fahmy al-Zaarir, the Fatah spokesman in the West Bank, said Naji had been visiting the camp before the attack.
Naji had been giving condolences to the relatives of two Fatah officials who had been killed during a shooting in the camp on Saturday. The shooting has been blamed on a family dispute.
Mieh Mieh camp was established in 1954 and is home to about 5,000 registered refugees, according to the UN Relief and Works Agency (Unrwa).
About 1.3 million Palestinian refugees who fled their homes during the 1948 Arab-Israeli war and subsequent conflicts, live in 58 refugee camps in Lebanon, Jordan, Syria, the West Bank and Gaza Strip.