Singapore intends to negotiate its territorial dispute with Malaysia in "good faith" next month, the island republic's Transport Minister Khaw Boon Wan said.

Khaw was quoted as saying by the Straits Times (ST) yesterday that he hoped that "good sense will prevail" and for the dispute to be managed in a "peaceful, calm and professional" manner.

Malaysia and Singapore have, of late, been involved in a dispute after Singapore claimed that Malaysia had extended the port limit of Johor Bahru port in a manner that encroached into Singapore Territorial Waters (STW) off Tuas on Oct 25.

Wisma Putra has refuted the allegation, saying it was well within Malaysia's rights to draw any port limit in its territorial sea, in accordance with Malaysia's own national laws.

Singapore retaliated by extending its own port limits on Dec 6, drawing protests from Malaysia. The republic's news reports also claimed that Malaysian vessels purportedly strayed into the republic's waters, and 14 such incursions were recorded between Nov 24 and Dec 5.

The two countries are expected to meet in the second week of January to discuss the maritime dispute, as well as another issue involving the Instrument Landing System (ILS), at the Seletar Airport in Singapore, that will come into force on Jan 3, 2019, which Malaysia claims will stunt development in the Pasir Gudang area.

According to Khaw, as of Monday, two Malaysian ships are still in Singapore waters.

"I don't think it is a question of counting one, two (or) three (ships). I think our preference - in fact, that is what we urged them to do - is to withdraw all the ships, because it's not conducive," he was quoted telling reporters after an interview session.

Khaw added that Malaysia's presence in the disputed area was worrying, as "accidents can happen".

"Unfortunately, they (Malaysia) do not agree to withdraw. So we will see how the bilateral discussion goes. My own view is it is not conducive to the bilateral discussion."