Several images were shared online of what the Israel Defense Forces says are weapons found inside the MRI building at the Al-Shifa hospital.
The Israeli army has always claimed the militant group is using hospitals as cover for its fighters and set up its main command in and beneath Al-Shifa, the largest in the besieged territory.
Both Hamas and Al-Shifa staff deny the allegations.
Two and a half weeks after sending tanks and ground troops into northern Gaza, Israeli forces entered the hospital early on Wednesday.
In a statement, the IDF says also present were “technological assets, along with military and combat equipment“ in one department and ”an operational command centre and technological assets“ in another.
All items have been transferred for full review by the relevant authorities.
A spokesman added as its soldiers entered the hospital complex, they engaged with a number Hamas militants and killed them, without elaborating further.
The IDF says it is “continuing to operate in the hospital complex, while extracting intelligence information and preventing harm to the medical teams and civilians sheltering there”.
Footage emerging from Al-Shifa since last night’s raid begins with a military vehicle and a number of soldiers carrying boxes and equipment, including what looks like an incubator.
Mohammed Zaqout, director of hospitals in Gaza, said Israeli tanks were inside the medical compound and that soldiers had entered buildings, including the emergency and surgery departments, which house intensive care units.
Al-Shifa hospital has become a symbol of the widespread suffering of Palestinian civilians during the war between Israel and Hamas, which erupted after gunmen murdered some 1,200 people and seized around 240 captives in a surprise October 7 attack into southern Israel.
More than 11,200 Palestinians - two-thirds of them women and children - have been killed since the war began, according to the Health Ministry in Hamas-run Gaza, which does not differentiate between civilian and militant deaths. About 2,700 people have been reported missing.
US National Security Council spokesperson John Kirby said on Wednesday that Washington did not sign off on Israel’s raid on Al-Shifa hospital.
Kirby, responding to questions about the timing of the operation and his statement that the US knows Hamas militants shelter in hospitals, said: “We did not give an OK to their military operations around the hospital.
Speaking to reporters from San Francisco, where President Joe Biden was preparing to meet with China’s leader he added: “We don’t expect the Israelis to inform us.”