The court has ordered an inspection by a top forest official at the temple which owns over 40 elephants.
It has also ordered an audit of the way things are being run at the elephant centre of the temple.
The court also said no iron rods or bullhooks should be used by the mahouts on elephants and then posted the case for hearing on Tuesday.
The viral videos of two mahouts beating elephants with iron rods came to the notice of the court while hearing a petition moved by a petitioner who had earlier flagged up ill-treatment meted out to the elephants at Guruvayoor.
The videos went viral on Thursday, prompting the Devaswom authorities to suspend the two mahouts who were seen thrashing the two elephants.
One of the elephants mercilessly beaten while being given a bath is named Krishna. He was given to the temple by late former Chief Minister of Tamil Nadu J Jayalalithaa many years ago.
The second elephant which was beaten by a mahout is named Kesavankutty.
The court on Friday asked the temple authorities if they were aware of what was happening in their elephant centre.
It also pointed out that if it had not been for the visuals which surfaced on social media, the incident would have gone unnoticed and the hapless animals would have continued to suffer.
The court was informed that the thrashing of the elephants took place on January 15 and January 24.
IANS