Ahram Arabic news website reported that trains connecting the capital Cairo and the south have resumed activity shortly before midnight on Wednesday.
Train services had stopped from Aswan to Cairo earlier on Wednesday night.
The internal radio at Cairo's Ramsis train station, the country's main train hub, announced in mid-evening that the government has grounded all trains to a halt in order to ensure the public's safety.
The announcement said protests by demonstrators at Ard El-Lewa train crossing in Giza were the cause for the decision.
Tens of residents of the working class district, on the outskirts of the capital, had blocked the Lewa railway crossing to demand the government improve safety conditions on the tracks.
State officials rushed to the site of the protest and reportedly convinced the residents to end their action promising to invest in safety.
Lewa residents have been protesting for weeks to force the government to upgrade railway crossing safety in the wake of a deadly accident in early January when a train struck a taxi at an undermanned crossing in the area.
Egypt has been plagued by train accidents that left hundreds dead in the past ten years.