The issue has dominated discussions around the Egypt camp since the seven-times African champions were held to a 0-0 draw by Angola in their Group B opener, when Salah was substituted midway through the second half before leaving camp the next day.
Speculation intensified after Hassan said the substitution was made for "technical reasons", despite Salah's strong form since joining Turkish side Trabzonspor from Liverpool.
Local reports also linked the controversy to some of Hassan's previous comments about senior players, including goalkeeper Mohamed El Shenawy who he said "at one point was finished", prompting questions about the mood inside the squad.
However, Hassan struck a conciliatory tone ahead of the trip to Juba, underlining Salah's importance to Egypt's plans.
"I respect all the players, especially Mohamed Salah. He is an important and influential player, one of the team's key pillars, a great player and a vital member of the team, as well as one of the best players in the world," he told reporters.
The coach said 34-year-old Salah's absence against South Sudan had been agreed between them before the Angola match because of concerns over the artificial playing surface.
"We decided to rest Salah because of the artificial pitch. He had discussed the matter with me before the Angola match, and we agreed on it," Hassan said.
"We need Salah in the upcoming matches. The well-being of every player is my top priority, and I have great confidence in all the players," he added.
Egypt are seeking their first victory of the qualifying campaign as they bid to reach the 2027 Africa Cup of Nations finals in Kenya, Uganda and Tanzania.
