Cardinal Franc Rode said the pope "wanted to use Slovenia as an example for the whole Church to show that there will be no compromises concerning financial and other problems".
"A harder line towards clerics and bishops can already be noticed" in the Vatican, Rode was quoted by Slovenia's Delo newspaper as telling journalists after a mass in Italy Sunday for the Slovenian community.
Pope Francis last week sacked the Archbishop of Ljubljana Anton Stres and the Archbishop of Maribor Marjan Turnsek over a financial scandal that has reportedly left one archdiocese with a budget shortfall of 800 million euros (just over $1 billion).
Tiny Slovenia only has two Catholic archdioceses.
The Bishop of Novo Mesto, Andrej Glavan, who replaced Stres as acting head of Slovenia's Catholic Church, condemned the move, saying blame had "unjustly fallen" on the two archbishops.
Rode refused to respond to these remarks.
"The case is now closed... I don't think there will be other decisions or sanctions," he said on Sunday.
Slovenia has been plagued by scandals for the last few years, including allegations that Rode and the former Archbishop of Ljubljana Alojz Uran had fathered children, despite taking the vow of celibacy.