American diplomats here have concluded that a quarter of the homes in Jewish settlements in the West Bank and half of those in the Gaza Strip are empty, raising questions about the Israeli Government's contention that it is expanding the settlements to accommodate natural growth.

The American figures, disclosed by the daily newspaper Haaretz and confirmed by United States officials, were immediately denounced by Prime Minister Benjamin Netanyahu as groundless and dismissed by the Jewish settlers as false.

The settlements have long been one of the most contentious issues between the United States and Israel, and Mr. Netanyahu's determination to expand them has been criticized by American officials as hampering peace efforts because the settlements make it more difficult to negotiate a territorial compromise between Israel and the Palestinians.

After the disclosure today of the American findings, Edward Abington, the American Consul General in Jerusalem, said the reported vacancy rate ''strikes me as undercutting the argument that settlement expansion is based on natural growth and demand for housing.''