ROME  When Rome magistrates opened an investigation last week into the Vatican bank over transparency issues, it was not only a bold assertion of state over church, it also pointed to one of the Vatican’s greatest continuing challenges: facing modernity.

As in the sexual abuse scandal, in which for years the Vatican appeared to declare itself outside  or above  civil law, this time the issue is the Vatican’s famously opaque finances, which for the first time are being held to tightened European Union anti-money-laundering statutes.

While Europe remade itself after the Second World War, balancing its powers through treaties and linking itself together through banking agreements, the Vatican remains an anomaly as the last absolute monarchy in the West. But today, its ancient ways are running up against civil institutions that increasingly view the church as they do any other multinational.

“The Vatican has to understand that the world has changed,” said Donato Masciandaro, the head of the economics department at Bocconi University in Milan and an expert in regulations on money laundering. “If it doesn’t understand that the world has changed, it risks having violations every day against the anti-money-laundering norms.”