The proposed facility has faced fierce opposition from local residents and environmental groups who say they are concerned the plant could produce harmful radiation.
Lynas plans to ship the slightly radioactive ore to the plant in Kuantan from the company's Mount Weld mine in Western Australia.
Tuesday's approval follows the government's rejection of an appeal by activists against issuing the temporary operating license.
In its 74-page report, the seven-member parliamentary committee included 31 recommendations based on the safe and transparent operation of the plant.
The report said that plant workers would be exposed to radiation at an average dosage of 2 millisieverts a year, which is less than the permitted dosage of 20 millisieverts a year.
"The committee found that up to now all the safety, health and environmental aspects in connection with the project ... have been met," the report states.
"In fact, more stringent rules have been imposed on the plant than international standards."
But activist group Save Malaysia Stop Lynas denounced the parliamentary committee's decision.
"Malaysia will be tainted with a reputation for fast-tracking (a) hazardous and risky project at the expense of the environment, the population and even the local economy that has sustained the livelihoods of hundreds and thousands of people for decades," the group said in a statement.
But Lynas said that the parliamentary group's findings were "yet another affirmation of the science behind" its plant and "the safety features built into it," reports The Malaysian Insider Web site.
"We look forward to the issuance of the temporary operating license so we can demonstrate that safety to the Malaysian community," the company said in a statement sent to the newspaper.
It added that it would submit proposals to meet the new terms.
Lynas has said the refinery would meet nearly one-third of the world's demand for rare earths, 17 minerals used to manufacture such products as wind turbines, batteries for hybrid and electric cars, flat-screen monitors, missile guidance systems and mobile phones.
The facility is expected to help break China's monopoly of rare earths. While China's rare earths reserves represent one-third of the global totals, it supplies more than 90 percent of the world's supply of the minerals.
Global demand for rare earth elements is expected to reach 160,000 tons by 2016, up from about 105,000 tons last year, says an estimate from Industrial Minerals Company of Australia.