The justice ministry asked a local court in February to declare the Communist Party of the Philippines (CPP) and its armed wing, the New People's Army (NPA), "terrorist" bodies that Duterte had sought to destroy.
Authorities said on Thursday some businesses were using the island's drainage system to send untreated sewage into its surrounding turquoise waters.
"Let us agree on some fundamentals", Duterte said, adding that he was ready to spend money to "subsidise" the rebels.
More than 2million tourists visited Boracay for its beaches and nightlife previous year, generating about £760million in revenue.
Before resuming talks, however, he said the rebels must agree to a ceasefire, stop extortion activities and abandon their proposal for the creation of a "coalition government".
Budget hostel manager Manuel Raagas also told AFP: 'I am really in a quandary on how to handle six months of closure.
PAL said it will affect 42 flights per week to Kalibo and 52 flights per week to Caticlan which equivalent to 5,000 to 7,000 passengers seats per week.
"The tour guides have already complained that they have no more guests".
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PAL has adjusted its operations in support of the government's decision to temporarily close or limit access to Boracay for urgent major environmental rehabilitation of the island.
"Boracay is a national treasure", PAL President Jaime J. Bautista said in a statement.
Ramon Ang, president and chief operating officer of San Miguel Corp.
Ang stressed all concerned sectors, including government, businesses, developers, and its residents, must also look beyond the island and move to disperse tourism to nearby municipalities such as Caticlan and Nabas.
Ang said SMC's proposal to build a toll bridge from Caticlan-to-Boracay will help solve the Island environmental woes and bring about growth to other areas in Aklan.
The decision to shut down the island for tourists is expected to "pave the way for the island's restoration as a tourism paradise".
Located off the northern tip of the central island of Panay, Boracay's white sand, lively night scene and abundant water sports attracted almost 2 million visitors a year ago, with the largest contingents coming from China and South Korea.
Duterte, whose leadership style has been criticized as dictatorial, has castigated the local government and residents for "overzealous" development and permitting beachfront building with inadequate sewage and water treatment facilities.