Some State Department officials have “refused to fully implement” President Trump’s renewed crackdown on the Cuban government, according to a leading Republican lawmaker.

President Trump in June announced new sanctions on Raul Castro’s regime, and the Treasury Department said Wednesday those changes would take effect through a new set of regulations on Thursday. But Sen. Marco Rubio, R-Fla., offered only qualified praise for Wednesday’s announcement and said some in the State Department are making it clear they oppose Trump's plan.

The new rules are a partial reversal of former President Barack Obama’s policy, as they “cumulatively seek to channel economic activities away from the Cuban military, intelligence, and security services” without cutting off American engagement with the Cuban people. The regulations bar “direct financial transactions” with an array of entities closely tied to Cuban national security entities and restrict American tourism to the island.

“Unfortunately, however, bureaucrats in the State Department who oppose the President’s Cuba policy refused to fully implement it when they omitted from the Cuba Restricted List several entities and sub-entities that are controlled by or act on behalf of the Cuban military, intelligence or security services,” Rubio said in a statement.

"We have strengthened our Cuba policies to channel economic activity away from the Cuban military and to encourage the government to move toward greater political and economic freedom for the Cuban people," Treasury Secretary Steven Mnuchin said of the policy shift.

But Rubio countered that the new list of restricted Cuban entities had ignored some state-owned entities, including major hotels. “These include Gran Caribe Hotel Group and Cubanacan,” he said.

The State Department denied hampering Trump's policy goals, despite those omissions.

“The department listed those entities with which direct financial transactions would disproportionately benefit Cuba’s military, intelligence, or security services or personnel at the expense of the Cuban people or private enterprise in Cuba, consistent with U.S. national interests," a State Department official told the Washington Examiner. "Some entities controlled by the military, intelligence, or security services or personnel did not meet these criteria."

U.S.-Cuba relations have worsened in recent months, due to a series of mysterious attacks on American diplomats that left officials suffering from hearing loss and other “cognitive issues.” The State Department warned Americans against traveling to the island, given that some of the incidents took place in popular hotels.

“I remain confident that this effort by some in the State Department to undermine the President’s directive will be addressed,” Rubio said.

The State Department plans to update the Cuba Restricted List "periodically," but the official made no promises about the particular hotels Rubio mentioned.

"Generally speaking, we assessed how listing identified hotels would affect the Cuban people and whether doing so advances the interests of the United States, consistent with the directives in the [National Security Presidential Memorandum]," the official said. "The department intends to update the Cuba Restricted List periodically and will consider relevant information, as applicable, on a case-by-case basis.”