Putrajaya's Airbus Corporate Jet 319 bearing the registration number 9M-NAA can no longer be tracked on flightaware.com.
The website said the data was not available for tracking as "per request from the owner/operator".
The request to remove public access to the data came shortly after Malaysiakini highlighted 9M-NAA's trip across Australia, which coincided with Prime Minister Najib Abdul Razak's family vacation Down Under.
The last time the tracking data was available was on Tuesday, which showed 9M-NAA touching down at Sultan Abdul Aziz Shah airport in Subang Jaya at 10.17pm after taking off from Perth International Airport at 4.56pm local time.
The data was removed from the site yesterday.
When contacted, FlightAware said it offered blocking services on condition that the request is accompanied with a copy of the aircraft's registration.
It added that the flight tracking service also allowed private tracking for owners of the aircraft.
"This would allow for only authorised users on your account to view the flight activity. It would still be blocked to the general public," it said.
Prior to this, data from flightradar24.com, another tracking site, was also removed.
Apart from 9M-NAA, a Airbus Corporate Jet 320 with registration number 9M-NAB, which the prime minister had previously used, has also been removed from the tracking sites.
A trip of two weeks
On Dec 31, Malaysiakini highlighted Prime Minister Najib Abdul Razak's son Norashman posting photos on Instagram from Gold Coast and Perth on dates which were consistent with where the 9M-NAA was.
The plane took off from the Sultan Abdul Aziz Shah airport in Subang Jaya at 12.07am on Dec 22 and landed in Gold Coast, Australia, at 10.06am the same day.
However, the stop was brief as the aircraft took off from Gold Coast at 11.47am and landed in Brisbane at 12.09pm. The plane remained in Brisbane for four days.
On Dec 26, the Malaysian government jet took off from Brisbane at 9.11am and landed in Gold Coast at 9.35am.
Again, the stopover at Gold Coast was brief, lasting only two hours and 47 minutes.
The plane then departed Gold Coast at 12.22pm and arrived at the Perth International Airport at 2.47pm. It returned to Malaysia on Jan 3.
Deputy Home Minister Nur Jazlan Mohamed defended Najib's use of a government jet for his family vacation, stating that there were security considerations involved.- Mkini