Shankaracharya Swaroopanand's comments came two days after the Shani Shingnapur temple in Maharashtra state let women into the inner sanctum.
For centuries, the temple had been open only to men.
Last month, the Mumbai high court affirmed the right of women to enter and pray inside all temples.
Women's activists had led protests demanding entry specifically to the Lord Shani shrine.
"Women entered Shani temple's inner sanctum," news agency ANI quoted the 94-year-old as saying on Monday.
"The women are worshipping Shani in the temple. By doing so, Shani's eyes would fall on women and this would result in increase of rape incidents."
Women were kept out of the Shani Shingnapur temple for nearly 400 years and temple officials, in the past, had claimed that the ban was actually "to protect women since Shani emits radiation which can harm them and cause deformity in a foetus if a pregnant woman enters the temple".
Last year, temple priests carried out an elaborate ritual cleansing after a woman managed to gain entry inside and offer prayers.
The temple authorities relented after last month's Mumbai high court ruling that women had a fundamental right to enter temples, and said those trying to prevent them would be handed a six-month jail term.
Several temples in India preserve the tradition of barring entry to women and in recent months, courts have been considering legal challenges to the policy.
Shankaracharya Swaroopanand's statement has caused outrage in India with many taking to social media to criticise him:
There were a few messages of support too:

Pte Cheryl James, 18, from Llangollen, Denbighshire, was found with a bullet wound to her head in Surrey in 1995.
Her parents said a dispute over the ballistics evidence could only be resolved if her body is exhumed.
Coroner Brian Barker QC said he would wait for a doctor's report before he made the decision.
He told the pre-inquest review at Woking Coroner's Court that exhumation was a "difficult and unusual" step.
Alison Foster QC, representing Pte James' family, said her relatives were "really dismayed to be at this point today".
"From our standpoint, an exhumation would be necessary for you to carry out a full and proper inquiry."
Bullet fragments in Pte James' body were yellow, while the SA80 rifle she was armed with used red bullets, Ms Foster said.
"There is no actual evidence that it was an SA80 that caused the bullet wound to Cheryl," she added.
The coroner said the full inquest on 1 February would consider whether there were "shortcomings" with the barracks's policies on sexual behaviour, supervision of young females, drugs, alcohol and accommodation.
Another pre-inquest hearing is to held on 10 September.
Pte James was one of four soldiers found dead at Deepcut, in Camberley, between 1995 and 2002.
Surrey Police's request that her inquest should be heard alongside fresh inquests into the deaths of Privates Sean Benton, Geoff Gray and James Collinson was turned down.
A spokeswoman for the force said: "[Surrey Police] has now completed the review of disclosure documents relating to Pte James."
She said arrangements for the inquest were a matter for the coroner.
"Surrey Police is supportive of the view that there should be a thorough inquest into circumstances surrounding the death of Pte James and our thoughts remain with her family."
A Hindu religious leader's comment that allowing women into a shrine devoted to Lord Shani (Saturn) will increase rapes has drawn criticism.
[NEXT_CONCEPT]
The family of a soldier found dead at Deepcut Barracks has urged a coroner to let her body be exhumed so a "full inquiry" can be held into her death.