The U.S. has paused a munitions shipment to Israel, U.S. Secretary of Defense Lloyd Austin confirmed Wednesday, warning that a major Israeli operation in Rafah could change the U.S. calculus on security assistance.

Austin is the first senior administration official to publicly confirm the U.S. pause on military aid but added that no "final determination" has been made.

"We are currently reviewing some near-term security assistance shipments in the context of unfolding events in Rafah," Austin told a Senate subcommittee, emphasizing that supplemental funding the administration just passed is not in jeopardy.

"We've been very clear, senator, as you know, from the very beginning that Israel shouldn't launch a major attack on Rafah without accounting for and protecting those civilians that are hitting that battlespace. And, again as we have assessed the situation, we paused one shipment of high payload munitions."

Austin maintained that the U.S.-Israel alliance is "ironclad."

-ABC News' Chris Boccia

One of the three hospitals in Rafah, Al-Najjar, is no longer functioning due to the ongoing hostilities in its vicinity and Israel's military operation, according to the World Health Organization.

"Hospitals in the south of Gaza only have three days of fuel left, which means services may soon come to a halt," the WHO warned.

The closure of the border crossing continues to prevent the entry of fuel needed for aid operations; without fuel all humanitarian operations will stop, the WHO warned. Border closures are also impeding delivery of humanitarian aid into Gaza, the WHO said.

"At a time when fragile humanitarian operations urgently require expansion, the Rafah military operation is further limiting our ability to reach thousands of people who have been living in dire conditions without adequate food, sanitation, health services and security. This must stop now," the WHO said.

-ABC News' Will Gretsky

Israel said it has reopened the Kerem Shalom Crossing Wednesday for the entry of humanitarian aid into the Gaza Strip.

"Trucks from Egypt carrying humanitarian aid, including food, water, shelter equipment, medicine, and medical equipment donated by the international community are already arriving at the crossing. After a thorough security inspection by the security personnel of the Ministry of Defense Crossing Authority, the equipment will be transferred to the Gazan side of the crossing," Israel said in a statement.

Israel had closed the crossing after it said Hamas fired a rocket toward the area over the weekend, killing four Israeli soldiers.

-ABC News' Will Gretsky

Thirty people, including six children and eight women, have been killed and 146 others were injured in Rafah on Tuesday, a spokesperson for Al Kuwaiti hospital in Rafah told ABC News.

People in at least six neighborhoods have started evacuating in eastern Rafah.

"With more than 1.5 million civilians crowded into this sliver of land, an Israeli military escalation threatens to turn Rafah into a graveyard. We are calling for an immediate and sustained ceasefire to prevent more civilian deaths and injuries in Gaza and enable the urgent scale-up of humanitarian aid. The survival of civilians in Gaza depends on it," Avril Benoît, executive director of Doctors Without Borders USA.

Aid groups, including the International Rescue Committee, have called on Israel to halt its ground incursion in Rafah and across Gaza, warning that civilians have no place to go.

"The dire warnings of aid groups have materialized: Israeli forces have launched a ground incursion into eastern Rafah and have taken control of the Palestinian side of the border crossing. Over a million civilians are now in imminent danger and aid flow through the Rafah crossing has halted with no aid trucks entering since May 5," said Bob Kitchen, IRC vice president of emergencies.

"Already, dozens of civilians are reported to have been killed in overnight Israeli airstrikes on Rafah City, while hundreds of thousands more remain at grave risk from the threat of further conflict and a lack of access to life-saving assistance. It is unconscionable to target such a densely populated area, leaving 1.3 million people with no safe haven," Kitchen said.

-ABC News' Ellie Kaufman and Will Gretsky

Although the Biden administration said it expected the Kerem Shalom and Rafah gates to be at least partially opened for humanitarian aid by Wednesday, the State Department was much less optimistic. However, the U.S. vowed it would continue to press Israel to get both portals up and running again.

While Kerem Shalom reopened Wednesday, aid had not been allowed to pass through because of "logistical and security concerns on the ground," State Department spokesperson Matt Miller said during a briefing Wednesday. He also said fuel had not been able to enter Gaza through Rafah.

"We think it's critical that Rafah be open for fuel because without fuel deliveries into Rafah, humanitarian assistance that comes in through Kerem Shalom can't actually be delivered. The two are critically linked," Miller said. "We're continuing to push for that to happen."

Miller didn’t provide any updated timeline on when the U.S. expected the crossings would be functional again, but said it was imperative that Israel act to increase the amount of aid allowed into Gaza following what he described as a "fairly dramatic dip" this week.

"When it comes to the level of humanitarian assistance, the results as they are today are just unacceptable. There's no other way to put it," Miller lamented.

He continued, "We are making quite clear to the government of Israel that we need to see those decreases reversed. We need to get back to where we were, and we need to see the levels continue to increase and see those sustained, and that is why we need to see Kerem Shalom and Rafah opened."

-ABC News' Shannon Crawford