The remarks were slammed as "dehumanising" by Council on American-Islamic Relations (CAIR) executive director Nihad Awad, who said the president should apologise.
Biden was asked at a White House press conference whether the death count meant Israel was ignoring US appeals to reduce civilian deaths in its bombardment of Gaza.
"I have no notion that the Palestinians are telling the truth about how many people are killed," he said.
"I'm sure innocents have been killed, and it's the price of waging a war. But I have no confidence in the number that the Palestinians are using."
Awad, the CAIR director, said: "The Israeli government has openly admitted that it is targeting civilians and civilian infrastructure.
"Journalists have confirmed the high number of casualties, and countless videos coming out of Gaza every day show mangled bodies of Palestinian women and children – and entire city blocks levelled to the ground."
Omar Shakir, Israel and Palestine director for Human Rights Watch, said the Gaza health ministry's figures "generally are consistent with what we're seeing on the ground in recent days".
"We have been monitoring human rights abuses in the Gaza Strip for three decades, including several rounds of hostilities," he was quoted as saying by The Guardian.
"We've generally found the data that comes out of the ministry of health to be reliable."
The relentless Israeli bombing campaign against Gaza has killed 7,028 people as of 15:00 local time (12:00 GMT) on Thursday, the enclave's health ministry said.
The ministry released a report it says includes the names and ID numbers of all those who have died, except for the 281 whose identity remains unknown.
The health ministry of the Palestinian Authority, based in the occupied West Bank, has reported a similar Gaza death toll of 6,850 in data that ran to 09:00 local time (06:00 GMT).
Biden's remarks about the Gaza death toll come after he previously said he had seen images of "terrorists beheading children" after Hamas's 7 October surprise attack inside Israel.
The White House later clarified his comments, saying the president and US officials had not seen such photos, nor independently verified such claims.
Biden also passed comment after an Israeli strike was blamed for a deadly 17 October blast at Gaza's Al-Ahli Baptist Hospital.
He said that it seemed it was not done by Israel, but by "the other team".
However, a New York Times analysis has raised questions about an important video pointed to as officials with both US intelligence and Israel have argued a misfired Palestinian rocket was responsible for the explosion.
The newspaper said on Tuesday that the missile visible in the footage was "most likely not what caused the explosion", adding that it was "unrelated" to the hospital catastrophe.
Reuters contributed to this report.