State governments have been told to name and gazette uninhabited islands as well as coral and rocky reefs, atolls and shelves under their jurisdiction immediately.
They have also been told to place border stones or boundary markers to establish ownership and prevent the possibility of intrusion by foreigners.
This is because the status of 535 out of the 879 islands lying in Malaysian waters is still unknown.
The Urban Wellbeing, Housing and Local Government Ministry wants the certification done so Malaysia can stake its claim to the said territorial waters as well as the economic resources there.
The federal directives to the states are contained in "Guidelines on the Planning and Physical Development of Islands and Marine Parks" - a tighter version of directives introduced in 1996 - to safeguard marine life and the ecosystem in the fragile environment, among others.
The revised guidelines are also designed to address the effects of climate change and the rise in sea level, increasing threats to coastal areas and the protection of natural habitats.
On April 12, 2011, then deputy minister of Natural Resources and Environment Tan Sri Joseph Kurup was reported as saying that all the remaining unnamed islands in Malaysia would be gazetted by June 2011. This clearly did not take place.
Urban Wellbeing, Housing and Local Government Ministry secretary general Datuk Seri Arpah Abdul Razak said the new comprehensive guidelines, endorsed by the Cabinet and National Council for Local Governments, specifically spells out the provisions that state governments must comply with when developing these environmentally sensitive areas.
"The revised set of guidelines, among others, touches on an island's density, activities that are allowed and strictly prohibited, the minimum planning standards for all types of development, provisions to protect the environment, its flora and fauna and biodiversity," she said in the guidelines, a copy of which was obtained by The Star.
Malaysia's islands are divided into four categories - development, resort, marine parks and uninhabited.
According to the guidelines, records from the Survey and Mapping Department and the National Hydrography Centre show that there are 879 islands in the country. Of these, 418 are in the peninsula.
Two hundred and twenty of the 418 islands located in the peninsula are known to be uninhabited.
The authorities are however unable to certify the status of 42 of the 67 islands in Johor and all the 34 islands off Kelantan. Similarly, they are also in the dark over the status of 67 of the 69 islands of Sarawak and the 392 islands belonging to Sabah.
Although the revised guidelines are only applicable in the peninsula and Labuan, both Sabah and Sarawak were encouraged to adopt them.
Malaysia had to take the case of the Sipadan and Ligitan Islands to the International Court of Justice (ICJ) after Indonesia laid claim to them. In 2002, the ICJ issued a judgment in favour of Malaysia.
However, Malaysia lost the atoll Pulau Batu Putih to Singapore.
The latest directive came in the wake of fears by certain countries in the region that China was increasingly laying claim to most of the South China Sea.
This time around, tighter conditions have been introduced on any proposed development in the islands - from the construction of houses, hotels and chalets along the beach, highlands, river and mangrove areas.
For example, new residential areas cannot be built in areas that could be exposed to tsunamis.
Also, facilities required during an emergency such as hospitals, fire and rescue stations, airports and schools, community centres and district offices must be built far away from coastal areas.
More stringent procedures have also been put in place for the construction of golf courses, theme parks, recreational clubs, marinas as well as jetties.
Apart from getting detailed Environmental Impact Assessment reports and approvals from agencies such as the Department of Environment and Marine Parks Department, developers will also have to comply with a host of other conditions.
For example, the construction of golf courses and theme parks at marine parks and uninhabited islands is prohibited. Also, only resorts are allowed to own golf courses.
Sea reclamation is also not allowed unless it has its economic advantages and does not adversely affect the environment, the guidelines say.
Also, any reclamation work must first be referred to the National Physical Planning Council.
Such work will only be considered if it is for the construction of ports for national interest, to control erosion and does not affect the hydrology system.
According to the guidelines, reclamation to create artificial islands is also prohibited.
It goes on to say that a proper integrated solid waste management system, including ways to reduce, reuse and recycle as well as composting should be implemented on all resort islands.
Mini incinerators are only allowed on the big islands, provided a detailed EIA study has been done. Landfills are not allowed on uninhabited islands or marine parks.
Airstrips are not allowed to be built on marine parks or uninhabited islands. They can be built on a resort island but under strict EIA regulations.
"Due to rapid development in the islands and marine parks, we need a constructive set of guidelines to prevent any adverse effects to the environment.
"There should be a balance to physical development and protecting the environment without jeopardising an island's natural attraction," said the guidelines.