His release was confirmed on social media by Israel's National Security Minister Itamar Ben Gvir and by a medical source inside the Gaza Strip.
Al Shifa director Mohammed Abu Salmiya was detained in November.
Successive raids have seen the hospital where he worked largely reduced to rubble since Israel launched its assault on Gaza after the October 7 Hamas attacks on southern Israel.
Salmiya and the other freed detainees crossed back into Gaza from Israel just east of Khan Yunis, a medical source at the Al Aqsa hospital in Deir el-Balah told AFP.
Five detainees were admitted to Al-Aqsa hospital and the others were sent to hospitals in Khan Yunis, the source added.
An AFP correspondent at Deir el-Balah saw some detainees have emotional reunions with their families.
Israel's military said it was "checking" reports about the prisoner release.
However, National Security Minister Itamar Ben Gvir confirmed the release when he posted on X, formerly Twitter, that Salmiya's release "with dozens of other terrorists is security abandonment".
Israel has accused Hamas of using hospitals in the Gaza Strip as a cover for military operations and infrastructure.
The militant group, which has run the territory since 2007, denies the allegations.
In May, Palestinian rights groups said a senior Al-Shifa surgeon had died in an Israeli jail after being detained. Israel's army said it was unaware of the death.
The war started with Hamas's October 7 attack which resulted in the deaths of 1,195 people, mostly civilians, according to an AFP tally based on Israeli figures.
Israel's retaliatory offensive has killed at least 37,877 people, also mostly civilians, according to data from the health ministry in Hamas-run Gaza.
