GUATEMALA CITY — The president of Guatemala pushed the nation toward a constitutional crisis on Monday, ignoring an explicit order by the country’s top court while testing the bounds of the nation’s fragile democracy.

The court had ordered that the head of a United Nations-backed anti-corruption commission be allowed back into Guatemala, reversing orders from President Jimmy Morales.

But the government stood its ground on Monday, saying it would not allow the head of the commission, Iván Velásquez, a Colombian citizen, to return. Instead the government said the United Nations, which appointed Mr. Velásquez to oversee the International Commission Against Impunity in Guatemala, should pick someone else to head the mission.

The announcement not only defied the constitutional court’s unanimous ruling late Sunday, but it was also a challenge to United Nations Secretary General António Guterres. In a rebuke to the Guatemalan government, Mr. Guterres had said at the beginning of the month that Mr. Velásquez would remain at the head of the panel even though he was barred from the country.

At the root of the crisis are a series of corruption investigations by the commission that have rocked the core of Guatemala’s power structure, sending politicians, businessmen and even former presidents to jail.

The commission’s investigations were once helpful to Mr. Morales: They helped unearth wrongdoing by his predecessor and contributed to Mr. Morales’s surprising victory in 2015. But when an inquiry into illegal campaign financing focused on Mr. Morales directly, he made Mr. Velásquez persona non-grata and vowed to shut down the commission.

The fracas on Monday was the culmination of more than a year of conflict between Mr. Velasquez and Mr. Morales. At first Mr. Morales, whose brother and son are both awaiting trial on corruption charges brought by the commission, tried to expel Mr. Velásquez from the country. But the constitutional court, the nation’s top judicial body, deemed the move illegal.

For a while, the matter appeared to be resolved. But Mr. Morales said on August 31 that he would not renew the commission’s mandate. Four days later, the government also barred Mr. Vélasquez, who has been the head of the commission since 2013, from returning to the country.

To most legal experts, that violated the spirit of the earlier decision. And indeed, when the court took it up again on Sunday night, it unanimously ruled that any attempt to block the entry of the panel’s commissioner into the country was illegal.

But because the ruling did not mention Mr. Velásquez by name, the government decided to impose its own interpretation. The Interior Minister, Enrique Degenhart, was categorical on Monday, declaring, “It is important to set the condition that the Colombian citizen Iván Velásquez Gomez, will not enter” Guatemala.

Instead, Foreign Minister Sandra Jovel said Guatemala had asked Mr. Guterres to come up with a list of acceptable replacement candidates within 48 hours.

Polls show that the commission enjoys widespread support among Guatemalans. As if to underscore the effectiveness of the panel, which works alongside Guatemala’s attorney general to build corruption cases, the commission announced arrests in two corruption cases last week, including one involving a former mayor of Quetzaltenango, one of the country’s largest cities.

The government’s campaign against Mr. Velasquez — to the extent of defying the court — has set off alarms.

“If they resist obeying the court then we are talking about a technical coup,” said Karin Slowing, an independent analyst and columnist for the newspaper Prensa Libre. “We are talking about a rupture that can take us in any direction.”

If congress, which is largely hostile to the commission, supports the government’s defiance of the court, “the country’s institutions will break,” Ms. Slowing said.

The last time a president openly defied the constitutional court was in the 1990s, and the conflict was only resolved when the army stepped in on behalf of the judiciary to enforce its decree.

It is unclear what will happen this time. Mr. Morales is supported by a powerful cadre of former military officers, but the United States’ support for the commission, which was unqualified last year, has waned in recent months.

At the same time, public pressure has been a deciding factor on this issue within Guatemala. In 2015, hundreds of thousands of protesters took to the streets to decry corruption, and the president at the time, Otto Pérez Molina, was forced to step down and face charges brought by Mr. Velásquez.

Mr. Morales appears determined to avoid his predecessor’s fate, and he has shown a willingness to push the nation to the brink to do so.

Last week, protests against Mr. Morales swelled in the countryside, but were more modest in the capital, where the government deployed police officers and soldiers to control the crowds.

Ms. Slowing said that one reason for the more muted response in the capital was because the private sector, which ultimately supported the protests in 2015, has largely backed the government against the commission this time.