Mohammed Mansur, the Egyptian transport minister, on Tuesday announced that Hanafy Abdel Qawi had been fired and his deputy, Eid Mahran, suspended pending an investigation into the crash.
At least 58 people were killed and 144 injured when a passenger train slammed into the back of another using the same track in the town of Qalyoub, just north of Cairo, derailing carriages and setting one train ablaze.
Ahmed Nazif, the prime miniser, told reporters during a hospital visit to see some of the injured on Monday that an inquiry had been launched and the results would be known within 48 hours.
"Those responsible will be held truly accountable," he said.
Mansur also said a technical committee would be formed to study the causes of the crash and to prevent future accidents, the official MENA agency reported.
Monday's crash was just the latest in a series of transport disasters in Egypt, most of which have been blamed on negligence and poor maintenance.
The country's deadliest rail disaster occurred in February 2002, when a passenger using a stove set ablaze a train heading to the south, killing at least 361. The lack of emergency exits resulted in most passengers being trapped inside the burning carriages.
On February 3, a ferry sank in the middle of the Red Sea killing about 1,000 people in one of the worst maritime tragedies in recent years.
Shipowner Mamduh Ismail, a government-appointed member of the upper house and the ruling National Democratic party of Hosni Mubarak, the president, fled the country.
He was stripped of his parliamentary immunity in March, his assets were frozen a month later and he was made to pay compensation to the families of victims.
The fact that Ismail, who is believed to have close ties with the presidency, was allowed to leave the country had fuelled accusations that the state was involved at the highest level.
Monday's crash further inflamed the press and public opinion.
Gamal Badawi in the opposition Al-Wafd daily said: "The state is collapsing, and corruption and ruin is creeping into it."
Columnist Nabil Rashwan said in the independent daily Nahdet Masr that the Qalyoub crash "has opened the file of disasters for the thousandth time, and no authority is accountable, and there is no end to the reasons".
"After the blood dries and the files of the technical and criminal and forensic investigations begin to pile up... the whole issue will be forgotten"
Rose Al-Yusef daily
Abdallah Kamal of the Rose Al-Yusef daily predicted that government investigations would fail to address the true issues or condemn the real culprits.
"After the blood dries and the files of the technical and criminal and forensic investigations begin to pile up... the whole issue will be forgotten," he said.
Since last February there have been three major train crashes in Egypt, the most populous country in the Middle East where transport has a reputation of being dangerous.
About 6,000 people die in road accidents each year. A report by the transport ministry said they were the second-highest cause of death in the country.