Egypt's Transport Minister Hisham Arafat said on Saturday that a deadly train collision in Alexandria on Friday was caused by the Egyptian railway's manual-operation system and poorly developed infrastructure.

Arafat made the remarks in a meeting with Egyptian President Abdel Fattah El-Sisi to discuss the preliminary results of a probe into the crash, presidency spokesman Alaa Youssef said in a statement.

"Initial indications show that the collision is attributed to the reliance on humans for railway operation, as well as the lack of infrastructure development over decades," Arafat said.

The incident, which took place on the outskirts of Egypt's coastal city of Alexandria on Friday, left 42 people dead and dozens more injured. Transport ministry officials have said the crash was caused by a malfunction in one train that brought it to a halt, with another train smashing into it from behind.

A number of provincial railway operation officials have been suspended and two drivers questioned over the incident.

El-Sisi said those responsible "should immediately be held accountable and offered no leniency, regardless of their positions," the Saturday statement added.

The president urged a quick upgrade of railway infrastructure, including an electronic signal system to be implemented nationwide to "limit this kind of accident and improve passenger safety procedures."

Arafat said the ministry has bought new engines and carriages, adding that the ministry is investigating the reasons for train delays in recent months.