Some 700,000 Rohingya Muslims crossed the border from Myanmar's Rakhine State into Bangladesh after militant attacks in August sparked a military crackdown that United Nations and Western countries have said constitutes ethnic cleansing.
Many of the Rohingya ensnared in the 2015 boat crisis wound up in Muslim-majority Malaysia and Indonesia as Thailand stuck to a policy of not accepting the vessels.
The military chief also said the tensions in Rakhine were "fuelled because the Bengalis demanded citizenship", using a term that Rohingya activists reject as implying they are illegal migrants from Bangladesh.
The boat was restocked with essential supplies in Thailand on Sunday before setting back out to sea, on its way to Malaysia, Thai police said.
Thai officials said there were about 56 women, men and children on board and that the Rohingya would continue towards their destination.
Smoke rises from shelters as Rohingya refugees cook their dinner at Unchiparang refugee camp, near Cox's Bazar, Bangladesh January 11, 2018.
"We don't have any such intelligence about anyone leaving Bangladeshi shores for Malaysia by boat", he said. "They want to go to Malaysia".
Meanwhile, the UN High Commissioner for Refugees (UNHCR) said it was concerned about the safety Rohingya refugees on the boat.
"Given the poor weather conditions now prevailing in the waters off the west coast of the Thailand-Malaysia border, we are concerned for the safety of the refugees", said Caroline Gluck, a UNHCR spokeswoman based in southeast Bangladesh.
"We may allow them to come in and feed them ... our concern is that if we allow one boat in, we have to allow other boats in after that", Zulkifili told Reuters.
The UNHCR said it was in touch with Malaysian maritime authorities and was ready to provide any necessary assistance to the refugees when they arrived.
Rohingya, treated as undesirables in predominantly Buddhist Myanmar, used to flee by sea by the thousands each year.
Rights groups expect another surge in Rohingya boats sailing for Southeast Asia, even if not at the levels of the past.