Activists from the People's Democratic Party (PRD) were not contactable on Tuesday after military and civilians leaders accused them of being behind the riots in which at least three people died.
PRD membership numbers are not known, but some sources said it was probably the largest activist group on Indonesia's most populous island of Java.
Members of the group, which routinely uses Marxist rhetoric in its statements, are believed to include students from major universities across Java as well as professional activists.
Its office in south Jakarta was empty on Tuesday with neighbours saying the activists left suddenly on Saturday night.
A handwritten sign on a window said only: "The occupants have moved.''
"They have all gone into hiding. They are being used as a scapegoat by the military,'' one political activist close to the group, which is not a recognised political party, told Reuters.
Indonesia's coordinating minister of politics and security affairs, Susilo Sudarman, said on Monday the riots had involved a third party, "among others...the PRD. This is a synonym for the Indonesian Communist Party (PKI),'' he said.
The riots broke out on Saturday after police took over the headquarters of the legal opposition Indonesian Democratic Party (PDI) to evict supporters of Megawati Sukarnoputri, who had been ousted as leader by a government-backed faction last month.
President Suharto banned the PKI in one of his first acts after taking power in the wake of the failed September 1965 coup, which was blamed on the communists.
Historians estimated more than 500,000 suspected Indonesian communists were killed in army-backed pogroms in the late 1960s.
In an interview published in Forum Keadilan magazine on Monday, PRD chairman Budiman Sudjatmiko, 27, was quoted as saying accusations his group was communist were typical of those made by the army during Suharto's 30-year-old government.
"We ask for proof, facts and data that our organisation is communist. Our aims and programme is for multi-party democracy, parliamentary democracy. Prove that this is a communist programme,'' he was quoted as saying.
The PRD's labour wing, the Indonesian Workers Struggle Centre (PPBI), organised a strike involving more than 4,000 workers on July 8 over wages in Indonesia's second city Surabaya.
Three PRD activists remain in detention after at least 14 were arrested when police and military broke up the protest.
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