A federal grand jury returned a 99-count indictment today against Italian financier Michele Sindona, charging him with fraud and perjury in the 1974 failure of Franklin National Bank, the biggest bank failure in the nation's history'

The indictment charged that Sindona looted deposits of two banks he controlled in Italy to buy effective controlling interest of the banks parent, Franklin New York Corp., then took $45 million out of Franklin and falsified the bank's records to cover that up.

Sindona, 58, who lives in a suite at the Hotel Pierre here, is fighting extradition to Italy where officials want to charge him with taking $225 million from several banks he owned there.

Robert B. Fiske Jr., U.S. attorney for the 7th District of New York, said that today's indictment should not interfere with the extradition proceedings' Sindona is out on $3 million bail while he appeals the extradition order'

Also indicted with Sindona was his close associate Carlo Bordoni, who was a top official in Franklin as well rs in several other banks Sindona controlled in Italy and Switzerland. Bordoni pleaded guilty to other charges stemming from the failure. Several top Franklin officials were convicted several weeks ago of falsifying bank records to conceal foreign exchange and bond trading losses.

Just before its collapse in 1974, Franklin National was the 19th largest bank in the country, with assets of about $3.3 billion. It was taken over by European-American Bank, which today is the 27th biggest bank in the country.

The federal indictment alleges that in 1972 Sindona illegally took $40 million of deposits and general funds from two banks he controlled in Italy and used the money to buy one million shares in Franklin, about 21.6 percent of the oustanding stock.

The grand jury said that the funds were transferred to two Swiss banks -- Amincor Bank (which Sindona controlled) and Privat Kredit Bank. The Swiss banks then shipped the funds off to Fasco International Holding (a dummy company owned by Sindona) that in turn used the money to buy Franklin's stock. The transferred funds showed up on the Italian banks' records as time deposits at the two Swiss banks.

The indictment said Sindona used the same techniques in 1973 to get another $27 million to buy controlling interest in Talcott National Corp., a Chicago-based commercial finance company.

In October 1972, three months after he bought Franklin, he shipped $15 million of Franklin's funds back to one of his Italian banks, again using a Swiss bank intermediary and recording the $15 million transfer as a time deposit at Amincor'

The indictment charges that Sindona and Bordoni also lost $30 million of Franklin's money speculating in foreign exchange.

When Sindona wanted to sell Talcott to Franklin Bank, he falsified 16 months of bank records to hide foreign exchange and bond trade losses to fool federal regulatory officials. They turned down the request anyway.