Federal prosecutors are investigating whether Cardinal John P. Cody of Chicago illegally funneled up to $1 million in church funds to a lifelong friend, according to the Chicago Sun-Times.

Spokesmen for the nation's largest Catholic diocese yesterday "categorically" denied any wrongdoing, and the 74-year-old woman who purportedly benefited from the cardinal's largess called the allegations a "vicious joke."

The Sun-Times' copyright story, which filled six tabloid-sized pages in yesterday's editions, said Cody, 73, used church funds he alone controlled to finance, among other things, a vacation home in Florida for Helen Dolan Wilson.

It also said that through the years the cardinal has referred to Wilson as his cousin. When Wilson was 4 years old her mother died; about a year later her father married Cody's aunt.

The newspaper said the investigation began nine months ago when a federal grand jury subpoenaed the records of Cody, Wilson and the archdiocese. An assistant U.S. attorney in Chicago confirmed yesterday that an investigation is under way.

The paper said that Cody and the archdiocese have refused to comply with the subpoena.

In today's editions, the paper reported that Wilson was paid a secret church salary, ranging from $7,200 to $11,500 annually, during a six-year period when she lived in Chicago. Wilson claimed she was an "office manager" for the archdiocese of Chicago, the Sun-Times said.

The allegations created an instant furor. The archdiocese, which has 2.4 million Catholics, has accused the paper of an "anti-Catholic bias," and Wilson said of yesterday's account: "This will be the death of him."

Cody, the son of an immigrant St. Louis fireman, has led the Chicago archdiocese since 1965. He has declined to comment on the allegations.

He and Wilson, who is divorced, have known each other since childhood. As children, Cody and Wilson lived and played together in the same, mostly Irish, neighborhood of St. Louis.

The newspaper quoted church sources as saying that over the years Wilson--described as an attractive, strong-willed personality--became Cody's closest confidante and the dominant figure in his life.

It reported that after Wilson retired in 1969 as manager of a small administrative office for the archdiocese of St. Louis, she began living a life style that seemed well beyond her means.

Her church pension was $1,500 per year, and friends and co-workers say they knew of no other jobs she had held. However, when she moved to Chicago following her retirement, her financial picture brightened considerably, the newspaper reported.

It cited public records in Florida and Missouri showing that, from 1969 to 1971, Wilson spent more than $100,000 in cash on the construction of a winter home in Boca Raton, Fla., an investment in a small business and a loan to her son. (Wilson, whose 12-year marriage ended in divorce in 1939, has two grown children.)

The fashionable ranch-style home, equipped with a pool, is near the Boca Raton Hotel and Club, where Wilson has spent an average of $2,500 a year in membership and dining fees, the Sun-Times reported. She sold the house in 1972 and purchased a condominium apartment nearby, it said.

The paper also reported that in the past 11 years Wilson has maintained apartments in Chicago and St. Louis.

The Sun-Times' investigation, conducted independently of the grand jury probe, uncovered church documents showing that over a seven-year period ended in 1973, more than $1 million in church funds was deposited in two unaudited bank accounts controlled by Cody.

Funds deposited in the accounts reportedly were for gifts to missionary priests and for household expenses related to the cardinal's official residence.

The church, as a tax-exempt religious organization, is subject to federal laws that prohibit the spending of money improperly to enrich any individual.

Canon law, the church's legal code, requires bishops such as Cody to keep personal expenses and possessions separate from church-owned property, and forbids the co-mingling of funds. Cody's annual salary is $12,000.

The paper reported that rumors concerning the two special accounts controlled by Cody have been circulating within the archdiocesan hierarchy for years. It quoted unidentified church sources as saying that the accounting practices, which gave Cody exclusive control, were highly unusual.

The accounts were set up by Cody in the mid-1960s and still existed as of the end of last year. In recent years, however, the level of funds deposited in them has dwindled.

Cody has a reputation as a tough administrator, a builder of schools and seminaries and, while bishop of New Orleans, a firm enforcer of desegregation in Catholic schools, often against heavy opposition from parents.

In its lead editorial yesterday, the Sun-Times said that the church has known for some time that the paper was conducting its own investigation, and has been trying to deflect the impact of the probe with repeated attacks on the newspaper.

The Chicago Catholic, the official archdiocesan newspaper, recently accused the Sun-Times of threatening "the right of Catholics to worship as they choose," the editorial said.

The Sun-Times' editorial said yesterday that the paper was sensitive to the "shock and distress" its account would cause and said its research was "extraordinarily thorough and painstaking."

Today the Sun-Times reported that Wilson was paid a secret church salary during a six-year period when she leased and furnished a luxury apartment on Lake Shore Drive.

The salary reportedly ranged from $7,200 in 1969 to $11,500 in 1975, when Wilson abruptly vacated her 27th-floor apartment at Lake Point Tower east of the Loop and left Chicago, the paper said.

Wilson claimed she was an "office manager" for the archdiocese, but several church employes at the time said they never saw her working--either at the chancery office or at Cody's church-owned residence.

During this same period, Wilson spent the winter months at the two Florida homes she owned at different times.

Chancery employes and other archdiocesan officials who processed the regular church payroll account were unaware of Wilson's salary, which was higher than the annual pay of most archdiocesan employes, including almost all lay teachers, the Sun-Times reported. In fact, it said, her salary even exceeded Cody's.

Soon after her 1969 retirement from her job in St. Louis, Wilson moved into a two-bedroom apartment at Lake Point Tower. Her rent at the outset was $450 a month, and climbed to $635 by 1975, the paper said.

She began receiving the salary for the Chicago office manager's job soon after she moved in, but former and current chancery employes said they never saw her at the archdiocesan administrative offices, the paper reported.

The Sun-Times said it had learned that Wilson did receive some of her mail at the cardinal's mansion, and a doorman at her Florida condominium gave the mansion as her summer address in Chicago. Cody lives alone in the residence, the paper said.

Wilson abruptly moved out of Lake Point Tower when rumors of Cody's resignation or reassignment were rampant amid a crisis over his closing of four inner-city Catholic schools. The paper said Cody helped her break her lease.

In another development, United Press International reported yesterday that Wilson's son, David, wrote the $500,000 auto insurance policy for priests in the Chicago archdiocese. A spokesman for Cody confirmed the existence of the policy, which had been reported previously in the archdiocesan paper. David Wilson's commission was 2.6 percent, about $13,000, the first year, and .84 percent for renewal years.