Morales had arrived at the hospital on Tuesday night along with Vice President Nicolas Maduro in a convoy of vehicles escorted by troops on motorcycles, and the Bolivian leader left later on without speaking to journalists who were waiting outside the hospital.
"I wasn't able to meet him," Morales said at a news conference at the United Nations. "I was only able to meet the head doctor and his family, but my understanding is that they are very encouraged.
Morales added, however, that Chavez has been going through "the most difficult moments in his life" and is still facing serious health problems.
"Now that he's returned to Caracas it's a great relief," Morales said.
Chavez's return to Venezuela from Cuba was announced by the government on Monday after a 10-week stay on the island during which he underwent a fourth cancer-related surgery and treatment for complications including a severe respiratory infection.
The government hasn't released any images of the president since his return, and Chavez's long absence from public view has been stirring renewed speculation about a possible new presidential election if his illness eventually forces him to relinquish power. Chavez hasn't spoken publicly since before his Dec. 11 surgery.
It was the second time that Morales has tried to see Chavez since his latest surgery. The Bolivian leader traveled to Havana in December but later gave few details about the quick trip. The visits underscore Chavez's importance to a generation of Latin American leftists who consider the Venezuelan president the heir of Fidel Castro and his efforts to stand up to what they consider U.S. imperialism.
Morales sidestepped a question on whether he would take a more prominent role in the region, along with Ecuador's leftist President Rafael Correa, now that Chavez has been sidelined at least temporarily. But he became nostalgic when discussing how much Chavez and Castro had helped him institute policies of nationalization and other reforms when he first took office in 2006.
"It really does pain me that Fidel Castro is no longer president, and particularly as well now that my brother president Chavez is in a very difficult spot with his health," Morales said.
In Venezuela on Wednesday, Maduro spoke on television about the jubilation among Chavez's supporters who celebrated his arrival in the streets.
"Venezuela is filled with love and happiness because we have commander Hugo Chavez Frias here in our homeland," Maduro said. He recalled that Chavez had personally told his government officials in Havana that it was time for him to return home to continue his "complementary treatments" in Venezuela.
It remains unclear what treatments Chavez is currently receiving, though medical experts say it could be more chemotherapy or other sorts of drug treatments, depending on the type of pelvic cancer he is fighting.
His supporters have been showing their support writing celebratory slogans on the windows of buses and cars in Caracas, such as "Chavez is alive" and "He's back."
The Venezuelan government also sought to buttress the official stance that Chavez remains in charge by issuing a statement strongly criticizing the U.S. State Department for a spokeswoman's remarks about a possible transition in the country.
The Venezuelan government said the comments by State Department spokeswoman Victoria Nuland "constitute a new and rude interference by the government in Washington in the internal affairs of Venezuela."
Nuland referred to the possibility of a new presidential election in Venezuela when asked on Tuesday about Chavez's return from Cuba.
"It is obviously a matter for Venezuelans to decide how the transition is going to take place," Nuland told reporters in Washington. "Should President Chavez become permanently unavailable to serve, our understanding is that the Venezuelan Constitution requires that there be an election to seek a new president."
She said the U.S. government "would hope that that election would be free and fair and balanced."
Chavez's government said Nuland's statements "have generated deep indignation among the Venezuelan people." It said that "the only transition being proposed is the transition toward Bolivarian socialism" being pursued by Chavez's government
Venezuela's sharply worded statement contrasted with recent remarks by Foreign Minister Elias Jaua, who said in a televised interview on Sunday that Chavez has instructed diplomats to seek improved relations with the United States.
The U.S. Embassy in Caracas has been without an ambassador since July 2010, when Chavez rejected the U.S. nominee for ambassador accusing him of making disrespectful remarks. That led Washington to revoke the visa of the Venezuelan ambassador.
Despite such diplomatic tensions, the United States remains the leading buyer of Venezuelan oil.
Edith M. Lederer reported from the United Nations. Ian James in Caracas and Eva Font at the United Nations contributed to this report.