"The US government seeks equal treatment and freedom to travel for all US citizens regardless of national origin or ethnicity," State Department spokesman John Kirby said.
"Specifically, the US government remains concerned at the unequal treatment that Palestinian-Americans and other Arab-Americans receive at Israel's borders and checkpoints."
The comments came in response to a question about reports of US citizens, particularly those eligible for a Palestinian Authority ID card, being denied entry into Israel after landing at Ben Gurion Airport outside Tel Aviv.
He did cite warnings posted on the State Department website that note Israel views anyone "believed to have claim" to a Palestinian Authority ID card -- meaning anyone with a parent or grandparent born or who lived in the West Bank or Gaza -- as a Palestinian resident, whether or not they are also a US citizen.
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As such, they are required to enter via the Allenby Bridge on the Jordanian border rather than through the airport.
"Many Palestinian nationals or dual nationals seeking to enter via Ben Gurion have been sent back to the United States upon arrival," the wesbite warns.
"Some families have been separated as a result and other travelers have forfeited expensive airline tickets."
These observations are reflective of recent reports of some Palestinian-American travellers' experiences.
Kirby said this was an ongoing subject of discussions between the US and its ally Israel.
"We regularly raise with Israeli authorities concerns about the issue of equal treatment for all US citizens at ports of entry," he said.
Relations between the countries have cooled recently following the collapse of the Israeli-Palestinian peace process and the signing last month of the Iran nuclear deal, which Israel vehemently opposed.