US President Donald Trump said the ceasefire he brokered was still in place. Hamas leadership, he said, may not be involved in the violations.
Aid into Gaza was set to resume on Monday, an Israeli security source said, shortly after Israel announced a halt in supplies in response to what it said was a "blatant" violation by Hamas of the truce.
The Israeli military said it struck Hamas targets across the enclave after militants launched an anti-tank missile and fired on its troops, killing the soldiers. The strikes killed at least 26 people, according to local residents and health authorities.
The armed wing of Hamas said it remained committed to the ceasefire agreement, was unaware of clashes in Rafah, and had not been in contact with groups there since March.