The head of Spain's Bishop's Conference Antonio María Rouco Varela made the comments during a New Economic Forum breakfast in Madrid.
"The church always prays for heads of State, and the King as well," said Rouco Varela, who is also the Cardinal Archbishop of Madrid, in his speech.
"I think it's the best form of help we can give them at this moment, both to them as individuals and the institution."
At the forum, the cardinal also called for a change to the country's abortion laws.
In 2010, Spain's former Socialist government introduced abortion laws which brought Spain into line with much of Europe by letting women freely opt for abortion in the first 14 weeks of pregnancy.
But Rouco Varela said the laws urgently needed changing as "many innocent lives are at risk".
The top cardinal spoke went on to speak with regret of those people "who believe that a healthy young chimpanzee is worth more than the small handicapped child of a man".
Rouco Varela also used his speech on Friday to hope for an end to a situation where parents had to choose every year whether their children would attend school religion classes.
"It's an annual referendum that Catholic parents have to undertake and different to every other country in Europe where people enroll in this subject just once."
Speaking generally about the state of the relationship with the Spanish Government, Rouco Varela stressed that the Catholic Church didn't prescribe any particular political position.
"The relationship between the Government and the State is only about us being able to exercise our (Cathoic) mission with freedom," said the cardinal.
He also said the church could "help in the development of legislation on certain issues".
Asked about his relationship with Prime Minister Mariano Rajoy, Rouco Varela said the Bishop's Conference generally dealt with individual ministries.
"But the option is always there to pick up the phone."
In May, Rouco Varela took the unprecedented step of selecting eight priests to lock horns with Satan as expert exorcists.
Press agency EFE reported that the exorcists' specialist ghostbuster training would be led by Cesar Franco, one of the Madrid's three auxiliary bishops.