Putrajaya may have made public its displeasure over a China coast guard vessel violating Malaysian waters by anchoring in the South Luconia Shoal but such intrusions have apparently been more extensive than it had let on.

According to satellite images obtained by current affairs and defence magazine The Diplomat , China had an even larger coast guard ship operating at the Luconia Breakers (Hempasan Bentin).

This was separate from a smaller China coast guard ship Putrajaya had complained about earlier this month.

The Luconia Breakers is part of South Luconia Shoal (Beting Patinggi Ali), which is around 84 nautical miles from Sarawak and is within Malaysia's exclusive economic zone that extends 200 nautical miles out to sea.

The report said the intrusion which was not disclosed by Malaysian authorities, was by a 4,000-tonne 3401-class China coast guard ship spotted in February.

"A satellite image from Feb 13, 2015 shows the Chinese vessel stationed 3.5 kilometres from an elevated coral sediment feature within a site called Luconia Breakers.

"Because the feature may qualify as above-water, it may be of special value to territorial claimants.

"Malaysia-controlled pipelines from marine natural gas fields also pass within 30 kilometres of Luconia Breakers," said the report.

The report said the satellite images also showed the Royal Malaysian Navy's (RMN) approximately 1,800 tonnes Kedah-class patrol vessel shadowing the Chinese ship.

"Chinese Coast Guard ships of the same '3401-class' have recently been used by Beijing to wrest control of the Scarborough Shoal from the Philippines, and to blockade the Second Thomas Shoal, where a unit of Filipino marines has been stationed," reported The Diplomat .

It is unclear if the ship is still operating in Malaysian waters, since the satellite image was captured four months ago.

'Similar ship arm twisted Philippines'

The Chinese ship is significantly larger than the one revealed by Minister in the Prime Minister' Department Shahidan Kassim earlier this month.

According to defence magazine IHS Jane's Fighting Ships , Shahidan had referred to the 1,149-tonne, 77-metre long Haijing 1123 vessel .

The Royal Malaysian Navy (RMN) confirmed to IHS Jane's on June 9 that it had deployed a Laksamana-class guided missile corvette to monitor the smaller China coast guard vessel.

Specifically, Malaysia used the 62-metre KD Laksamana Hang Nadim, deployed on June 3.

"The Chinese vessel has been warned to leave the area and our ship is monitoring it very closely", a RMN spokesperson was quoted as saying by IHS Jane's.

Putrajaya had said it would file a protest to China over the June incident.

The Diplomat noted that Malaysia may have been reluctant to give public attention to the intrusions to avoid a similar standoff that happened between China and the Philippines.

"By not revealing this shadowing of the more threatening Chinese ship, Malaysia may wish to avoid a full-fledged stand-off like the one that resulted in the Philippines losing the Scarborough Shoal in 2012.

"The Malaysian leadership may also be weighing whether over time it can benefit from a counterbalance from the US and its allies," it said.

'M'sia silent on past intrusion'

This is not the first time China had intruded into Malaysian waters.

Last January, Reuters reported three Chinese ships entered the James Shoal, coming within 80km of Sarawak.

However, Malaysia did not file a protest over the intrusion nor did it acknowledge the incident.

Instead, Chinese foreign ministry spokesperson Qin Gang was the one who confirmed the incident to the Singapore media.

Qin claimed the territory is an "indisputable sovereignty" of China and pointed out that Malaysia did not lodge any official protest, according to Singapore Straits Times.

China has been at odds with several countries surrounding the South China Sea as Beijing claims large swathes of the oil-rich region as its own.

Countries like Vietnam and Philippines have had skirmishes with the Chinese maritime forces but are wary of escalating any conflict with the superpower.

The US, a close ally of the Philippines, is the only country willing to challenge China in the Southeast Asian region.

Last month, the US flew a spy plane over vast reclamation areas that Beijing is developing in the South China Sea to strengthen its claims over the region and extend its own exclusive economic zone.