The announcement came more than two months into the Israel-Hamas war in Gaza as international aid organisations have warned about the dire conditions in the crowded Palestinian territory.
The ministry did not specify which vaccinations had run out, and its claim could not be independently verified.
The UN Humanitarian Coordinator for the Palestinian territories, Lynn Hastings, said that UNICEF was looking into the issue.
"Vaccinations are one of the priority items that we are trying to bring in to ensure that we are able to continue with the vaccine campaign," Hastings told journalists at an online briefing without elaborating.
Tedros Ghebreyesus, head of the World Health Organization, warned Sunday that "Gaza's health system is on its knees and collapsing," with 14 of 36 hospitals only partially functioning and supplies running low.
"The risk is expected to worsen with the deteriorating situation and approaching winter conditions," he said.
The Gaza health ministry called on international institutions to deliver urgently needed vaccines "to prevent disaster".
Israel has waged a 68-day war against Hamas, which rules the Gaza Strip, since its gunmen launched the October 7 attacks.
Those attacks killed at least 1,200 people in southern Israel and the militants took around 240 people hostage, according to Israeli officials.
Israel's bombing and ground offensive since has killed over 18,400 people in the Gaza Strip, mostly women and children, according to the health ministry.
