Finance Minister Lim Guan Eng issued a statement announcing the "suspension notice" on the East Coast Rail Link (ECRL) and the two pipeline projects after seeking advice from Attorney General Tommy Thomas.
Malaysia suspended three of its largest China-backed projects worth $22 billion on Thursday.
Malaysia's previous government under Najib had cultivated warm ties with China and signed a string of deals for Beijing-funded projects.
East Coast Rail Link will connect the South China Sea in the east coast of Peninsula Malaysia with strategic shipping routes in the west and is a major part of China's infrastructure push across Asia and beyond. The rail line was to stretch 688 km (430 miles) and join the two coasts of Peninsular Malaysia at a cost of 55 billion ringgit ($13.5 billion).
The suspension came just a day after Finance Minister Lim Guan Eng called for a sharp price reduction in the 688-kilometer East Coast Rail Link after discovering that the project's actual cost is 81 billion ringgit ($20 billion), almost 50 percent higher than that estimated by the previous government.
"The decisions are exclusively directed toward the related contractors, relating to the provisions mentioned in the agreements, and not at any particular country", the finance ministry said in a statement on Thursday.
Najib was charged on Wednesday with three counts of criminal breach of trust and one count of power abuse in relation to RM42 million allegedly misappropriated from a former 1MDB unit.
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Washington says the measures are a response to intellectual property theft by China. The stock is responding favorably, up $1.79, or 3.5%, at $53.27, in early trading.
"The terms are very damaging to our economy", he said at the time.
The new Malaysian government, led by Mahathir Mohamad, has disclosed in recent weeks how the Najib administration used federal agencies and government money to bail out debt-ridden 1MDB, which is being investigated in at least six countries.
A Malaysian foreign ministry source said both sides had yet to finalize dates, but Mahathir was "looking forward to visiting China".
"We respect and comply with Malaysian laws".
In addition to the ECRL, the finance ministry yesterday confirmed that two pipeline projects awarded in 2016 to China Petroleum Pipeline Bureau, together worth $2.3bn (9.4 billion ringgits), had also been suspended, The Edge Markets reports. "Under the situation we have no choice but to adhere to the suspension instruction", it said.
"During this period of suspension, you shall protect, store and secure the works against any deterioration, loss or damage".
In May, he postponed plans to build a high-speed rail link between Singapore and Malaysia, which had been agreed on several years ago, saying it was expensive.