Mr Williams is to be charged along with his technical director Patrick Head, the Williams chief designer Adrian Newey and three other people, it was announced last night.
Senna died from fatal head injuries when his Williams-Renault crashed at 190mph after running off the Tamburello curve at the Imola track during the grand prix on 1 May 1994.
Responding to yesterday's announcement, the Williams team issued a statement, saying: "We do not believe the charges are well-founded and intend to do all that is necessary to defend our position and contest the charges." The team's Italian-based lawyer Roberto Causo added: "We deny the charges absolutely."
Mr Causo refused to say whether any of his clients would attend the trial. Under Italian law defendants have the right to stay away from any proceedings against them.
The first hearing has been scheduled for 20 February in Imola, nearly three years after the death of Brazil's three-times former champion.
The Belgian race director Roland Bruynseraede, the Imola race track director Federico Bendinelli, and a former track official, Giorgio Poggi, have also been charged with manslaughter. They also deny the charges.
The maximum sentence for manslaughter in Italy is seven years, although it is thought anyone convicted over Senna's death would be given two-year suspended sentences.
But the decision to press ahead with manslaughter charges after a two- and-a-half year investigation could have serious consequences for motor racing in Italy and next season's Formula One championship.
Benetton's team chief Flavio Briatore said he would boycott Italy's two grand prix races if any of the Williams personnel were convicted over the death.
"If anyone were to be convicted in Italy, it would be big trouble," Mr Briatore said last week. "I would not risk bringing my team to a country that can convict you for an accident. Fatality is part of the game."
But Mr Williams, speaking last month, said it would not have any bearing on whether his team raced again in Italy. "The law is above motor sport," said Mr Williams, whose team this year won a record-equalling eighth constructors' title and powered Damon Hill to the drivers' crown.
"As to whether we go back there or not, I have absolutely no view whatsoever. Wherever the calendar schedules races we will be there. Ostracising Formula One in Italy will not change the law."
The formal charges mark the latest stage in a complex investigation led by the Bologna magistrate Maurizio Passarini, which has suffered many leaks.
Much of the speculation has centred on the possibility of structural failure with a faulty weld on the steering column snapping off, sending the car out of control.