President Joe Biden said on CNN Wednesday that American bombs have been used to kill civilians in Gaza and doubled down on the administration's plan to withhold weapons that Israel could use in a Rafah invasion.

Following the news that the U.S. has paused a munitions shipment to Israel, CNN anchor Erin Burnett asked whether any of the U.S. bombs sent to Israel have been used to kill civilians in Gaza.

"Civilians have been killed in Gaza as a consequence of those bombs and other ways in which they go after population centers," Biden responded.

"I made it clear that if they go into Rafah -- they haven't gone in Rafah yet -- if they go into Rafah, I'm not supplying the weapons that have been used historically to deal with Rafah, to deal with the cities, that deal with that problem," he continued.

Biden said the U.S. will "continue to make sure Israel is secure in terms of Iron Dome and their ability to respond to attacks that came out of the Middle East recently."

"But it's, it's just wrong," he said. "We're not going to -- we're not going to supply the weapons and artillery shells used, that have been used."

Burnett also sought to nail down Biden's view of what Israel is doing in Rafah right now, and if the president believes that qualifies as a major ground invasion.

"No, they haven't gone into the population centers," he said. "What they did is right on the border. And it's causing problems with, right now in terms of -- with Egypt, which I've worked very hard to make sure we have a relationship and help."

"But I've made it clear to Bibi and the war cabinet, they're not going to get our support, if in fact they go in these population centers," he continued.

-ABC News' Molly Nagle

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

The Gaza Health Ministry said its medical teams have found a third mass grave inside Al-Shifa Hospital's medical complex.

The health ministry has recovered 49 bodies so far as the exhumation process continues.

The ministry said this is the seventh mass grave found by medical teams inside hospitals — one in Kamal Adwan Hospital, three in the Shifa Medical Complex and three in the Nasser Medical Complex. A total of 520 bodies have been recovered from the graves.

In April, the Israel Defense Forces denied accusations from the ministry that they buried at least 283 bodies in a mass grave near Nasser Hospital in Gaza. The IDF alleged that during its operation near the area of Nasser Hospital, it examined corpses in that area in an effort to locate hostages.

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