Wazir serves as head of the Armed Forces Engineering Authority, one of the main owners of the new administrative capital being built outside Cairo and a developer of large infrastructure and national projects commissioned by Sisi, Presstv Reported.
The previous minister, Hisham Arafat, stepped down immediately after the Feb. 27 crash, in which a locomotive smashed through station buffers and burst into flames, killing at least 22 and injuring dozens.
"When this (the accident) happened, we said the person who will take over (the ministry) is Kamel al-Wazir," Sisi said during a seminar organized by the armed forces to celebrate martyrs' day.
Sisi told Wazir, who frequently appears alongside the president at public events, that he can call upon any support he needs to revamp the rail system from all state institutions, including the military.
"If you want officers from the vehicles administration, the armored vehicles or the engineers .. I don't have a problem," he said, as he turned to Defense Minister Mohamed Zaki, who was also on stage along with the speaker of parliament.
He then promoted Wazir from major general to lieutenant general, pinning new epaulettes on his uniform.
The appointment is part of what analysts say is a broader trend to expand the role of the military since Sisi led the 2013 military overthrow of Egypt's first freely-elected president, Mohamed Morsi of the Muslim Brotherhood.
Parliament is currently debating proposed constitutional changes that could allow Sisi to stay in power until 2034 and tighten his control over the judiciary.
The changes include amending article 200 of the constitution to add that the military has a duty to protect "the constitution and democracy and the fundamental makeup of the country and its civil nature".
The military's economic and civilian activities have expanded since Sisi became president in 2014, and companies owned by the military have flourished, causing concern amongst local businessmen and foreign investors.
"This trend is rooted in the claim that the military is uniquely capable of delivering results," said Timothy Kaldas, non-resident fellow at the Tahrir Institute for Middle East Policy.
"(This), in turn, justifies the military's expanding control over state institutions and participation in the economy as its businesses and enterprises continue to grow and diversify," he added.