Spokesman Fuad Basya said the boat had run out of fuel but that "permission was not given to that boat to land." He said he had no information about its current location.
It was not clear if the boat was the same one -- said to be carrying 400 people -- that Indonesian search and rescue officials told CNN they had sent teams "to help evacuate" in the early hours of Monday morning.
A spokesman for the International Organization of Migrants, Steve Hamilton, said the organization had been trying to seek information about the boat carrying 400 people but had so far drawn a blank.
"We checked with all the authorities and we have no information about the boat. It didn't materialize," he said. He added that they had heard rumors that the navy had encountered and refueled a boat but had no further information.
Indonesian military spokesman Basya said that the navy had initially wanted to turn away another group of migrants who landed at Lhokseumawe City but they were told by the Ministry of Foreign Affairs that they couldn't do that.
On Sunday, 547 people traveling on six boats were found at sea off Lhokseumawe City, in Aceh, Indonesia. They are now being processed in a number of migrant shelters on land.
Stranded at sea
It's thought that as many as 8,000 people could be being held at sea by smugglers attempting to evade arrest during a Thai government crackdown on the industry, according to Jeff Labovitz, another IOM spokesperson.
"Every landing we generally receive some health issues. But whenever there are delays... then we see severe deterioration, because those people are often beaten too, and they're not given food because that is a methodology to get them to pay," Labovitz said
In recent weeks, Thai authorities have raided camps along the border with Malaysia, where smugglers have been known to keep human cargo while they wait for payment, including ransoms for relatives in return for their captives' freedom. Last week they made a gruesome discovery; a mass grave containing 26 bodies at a camp in the Sadao district of Songkhla province.
Human Rights Watch said the bodies were of Bangladeshi and Rohingya migrants who had "starved to death or died of disease while being held by traffickers who were awaiting payment of ransoms."
Labovitz said the closure of the "Thai corridor" had deterred "ruthless" smugglers from attempting to dock, so they stayed at sea as supplies dwindled and conditions worsened.
During a press conference on Monday, Thai Army Chief General Udomedej Sitabutr said the army had been instructed to search for more illegal migrants camps along the border, and to seal off the Thai coast to illegal entry.
He said tackling human trafficking was a top government priority and that more arrests had been made as it continues its investigation into the trade.
Boats rescued off Aceh
On Sunday, 547 people were found on six boats off Lhokseumawe, in northern Aceh. "They were drifting out at sea for a days, maybe even longer, without food and water. Many of them are weak and depressed. There a number of very young children too," said Tegas, an officer at the North Aceh Immigration Office, who only goes by one name.
The boat people were economic migrants from Bangladeshi and stateless Rohingya Muslim refugees from Myanmar, also known as Burma, according to the IOM, which is helping the government to care for the migrants in shelters in the nearby city of Lhoksukon. They're soon to be moved to Paya Batung, about 13 kilometers (eight miles) away.
Another group of more than 1,000 migrants landed on the tourist resort island of Langkawi off the coast of Malaysia. They too are from Myanmar and Bangladesh, according to Malaysian police.
The flow of migrants from both countries has surged in recent months, according to the UNHCR
. In the first three months of this year, 25,000 attempted to make the perilous journey by boat from the Bay of Bengal to Malaysia and Thailand, the agency said. Based on survivor accounts, it estimates that at least 300 of those have died from starvation, dehydration or abuse by crews.
Fleeing Bangladesh and Myanmar
According to the UNHCR, migrants say the most common route takes them to the Ranong area of Southern Thailand. From there, they're taken on a one-day road journey to smugglers' camps on the Malaysian border.
Money was likely to be extorted from them along the way, with the false promise of paid work or cash when they arrived, the UNHCR said. In reality, many are kept in "horrific conditions" at camps until relatives pay for their release.
Last year, the U.S. State Department downgraded Thailand to the worst possible ranking -- tier 3 -- in its Trafficking in Persons (TIP) report.
It said Thailand was a source, transit point and destination for trafficking. The report also said that ethnic minorities and citizens of neighboring countries were especially at risk of exploitation in Thailand through forced labor or the sex trade.