Soon after he took up his post in El Salvador, U.S. Ambassador Ronald Johnson forged an unusually close relationship with the country’s president.

President Trump had nominated Mr. Johnson in 2019 as his ambassador to the country shortly after the White House declared war on El Salvador’s notoriously violent gangs, including MS-13.

The relationship between Mr. Johnson and the Salvadoran president, Nayib Bukele, was close enough that it worried some officials. The two posted photos on social media of their families spending weekends together and tweets highlighting their “personal friendship.”

That bond remained firm even in 2020 when the Salvadoran president was accused of secretly colluding with local gangs, seven current and former officials said. Mr. Johnson defended him and publicly dismissed a letter from U.S. Republican congressmen raising concerns about the claim.

Then, without clear reason, a U.S. Embassy staff member investigating the government’s potential ties to the gangs was sent home early.

The ambassador’s actions seemed to contradict the interests of the Trump administration, argued three current and former American officials who worked directly with Mr. Johnson. He appeared more focused on protecting a foreign leader, the officials said, than on dismantling the Salvadoran criminal organizations operating both there and within the United States.