Hamas officials on Saturday said the move was not meant as a provocation.
But Abbas' Fatah movement said the deployment risked igniting new violence.
The 3,000-strong Hamas militia has been at the centre of the Palestinian infighting. Hamas' decision to withdraw the black-clad force on Friday, which was banned by Abbas, was widely seen as a conciliatory gesture.
Youssef Zahar, spokesman for the militia, said Saturday's deployment did not contradict the previous day's decision. At the time, Hamas said the force would remain on standby at fixed locations and resume limited patrols in the future.
"The police stations are closed to us, so we're making use of some streets," Zahar said.
The Gaza Strip has been plagued by armed chaos and lawlessness since the Israeli army cracked down and destroyed much of the Palestinians security infrastructures in retaliation for the Palestinian uprising
Israel did withdraw from the Gaza Strip last autumn but still controls the borders, air space and sea of the Palestinian territory whose economy is in tatters.
The presence of the Hamas gunmen was much smaller than earlier this week, with forces stationed at several major intersections and near the homes of senior Hamas government officials.
The situation appeared to be calm on Saturday, and in some instances, Hamas gunmen were seen chatting freely with regular policemen.
Fatah spokesman, Tawfiq Abu Khoussa, however said the return of the Hamas force, even in small numbers, was "unacceptable and illegal."
"The lack of its presence on the streets yesterday brought great relief. Their return signals the possibility of new friction," he said.
In Gaza City, hundreds of militants from the Abu Rish Brigades, a group loosely linked to Fatah, gathered near the parliament building to demonstrate against the Hamas force.
"This force is unacceptable," said Abu Harun, a spokesman for the group. The crowd, which included some armed men, dispersed peacefully after the protest.
The Fatah spokesman accused Hamas of trying to carry out "political extortion" as the two sides continue their dialogue aimed at ending the standoff.
Abbas has been locked in a power struggle with Hamas since the Islamic group defeated Fatah in legislative elections in January.
Abbas, elected separately last year, has been seeking to curb Hamas' authority in security matters and other areas.
Hamas decided to form its militia in April after Abbas placed a loyalist in charge of forces that report to the Hamas-controlled interior ministry.
The militia was deployed for the first time last week, setting off days of clashes with Fatah-dominated security forces that left 10 people killed.