"For the time being, Mr. Pierre Gauthier will manage the responsibilities of Mr. Gainey with the Canadiens," said a statement from the NHL club.
"In respecting the privacy of Mr. Gainey and his family, the Canadiens will not issue any further comment at this time."
Gainey, a Hall of Fame player who was named the Canadiens GM in 2003, was with his three other children, Anna, Colleen and Steve, as rescuers searched the U.S. coast south of Cape Cod.
Laura Gainey, 25, was swept off the tall ship Picton Castle by a large wave during a storm on Friday night. The searched continued as hope dwindled of finding her alive.
The Canadiens players and coaches were given Sunday off and were not available for comment. They are scheduled to practice Monday morning at the Bell Centre.
It is a second major crisis for the Gainey family.
In 1995, Gainey's wife Cathy died after a five-year battle with brain cancer, when she was 39.
Laura is the third of Gainey's four children.
Having Gauthier step in at least puts the NHL club in experienced hands until Gainey is able to return.
Gauthier, 53, was named assistant GM this season after serving as a pro scout in 2005-06. The Montreal native was president and GM in Anaheim from 1998 to 2002 and was GM of the Ottawa Senators from 1995 to 1998. He was also assistant GM in Anaheim from 1993 to 1995.
"He knows the role and he's comfortable in it," said Craig Button, a pro scout for the Toronto Maple Leafs who worked with Gainey when the former Canadiens captain was GM in Minnesota and Dallas.
"He can certainly fulfill the obligations of that position in Bob's absence."
Button was shaken by the news of Laura Gainey's disappearance and said "you pray for them to find the strength to get through this together."
With Gainey attending to his family, Gauthier was at the Bell Centre for the Canadiens' 3-2 shootout loss to Buffalo on Saturday.
The team also has vice-president of hockey operations Julien BriseBois, a lawyer who handles contracts and matters related to the Collective Bargaining Agreement with the players.
Gainey, who turns 53 on Wednesday, won five Stanley Cups from 1973 to 1989 with Montreal. He won the Frank Selke Trophy as the league's top defensive forward the first four years it was awarded from 1978 to 1981.
He joined the Minnesota North Stars, now the Dallas Stars, as head coach in 1990 and added the GM title in 1992. His Stars won a Stanley Cup in 1999.
His son Steve Gainey, 27, was drafted in the third round by Dallas in 1997, but spent most of his career in the minors. He signed with the Phoenix Coyotes in 2005 and played 20 games last season. He is not playing this season.
In his NHL career, Steve Gainey has no goals and two assists in 33 games.