KUALA LUMPUR/SINGAPORE (Reuters) - Malaysia has told Singapore it intends to take back control of airspace that the city-state has managed since 1974 amid a dispute over a flight path to a secondary airport in Singapore, Malaysia’s transport minister said on Tuesday.

Singapore has put in place a new instrument landing system at its small Seletar airport to be used by turboprops and business jets that involves a flight path over Malaysian airspace without its permission, Malaysian Transport Minister Anthony Loke told parliament.

He said the flight path would lead to height limits on building development and affect shipping operations in the state of Johor on the south of the Malaysian peninsula that borders the relatively tiny island of Singapore.

Malaysia refused to approve the flight path on Nov. 28 and 29, Loke said, and on Nov. 29 informed Singapore it planned to take back airspace over Johor, that it had delegated for management by the city-state since 1974, in phases, with the first expected around the end of 2019 and the next phase in 2023.

“We feel that it is now the time that we regained the control of our very own airspace because over the years, we have also upgraded our air traffic control and we think we are capable of doing so,” he said. “So we want to begin the process of negotiations with our Singapore counterpart.”

Loke did not provide details of what airspace Malaysia intended to regain in each phase.

The Singapore transport ministry said in a statement in response to Loke’s comments that Singapore “respects Malaysia’s sovereignty”.

“Airspace in this region is one of the most complex in the world… The benefits to both our economies and our people have been tremendous…. Hence, any proposed changes will impact many stakeholders,” it added.

Singapore’s far larger and newer Changi Airport, one of the biggest hubs in Asia, uses a portion of that airspace for departures and approaches and would not want to be reliant on Malaysian management of it, said an industry source who expected they would settle the dispute before it got to that stage.

Singapore was once part of Malaysia but they separated acrimoniously in 1965, clouding diplomatic and economic dealings for years. Ties were particularly frosty during Malaysian Prime Minister Mahathir Mohamad’s previous tenure as prime minister, between 1981 and 2003.

Since returning to office after an election this year, Mahathir has deferred a rail project with Singapore and has said he wants to renegotiate the terms of a water-sharing agreement struck in 1962.

Just hours after Loke’s comments, Singapore hit back with its own territorial protest against Malaysia over Kuala Lumpur’s plan to extend the limits of a port in its southern-most state.

“We note with grave concern that Malaysia has recently purported to extend the Johor Bahru port limits in a manner which encroaches into Singapore Territorial Waters,” it said in a separate statement.

“In response, Singapore has lodged strong protest with the Malaysian Government,” the transport ministry added.

A Malaysian foreign ministry spokesman declined to comment on Singapore’s protest, and directed queries to the transport ministry. A spokesman for Loke declined comment.