The Magpies are deep in the relegation mire despite a significant outlay last summer and in the January transfer window, sitting 19th in the Barclays Premier League and one point from safety.
A 3-1 defeat to Bournemouth on Saturday appeared to be the final straw for a mutinous St James' Park crowd, as supporters turned on under-pressure head coach Steve McClaren.
The former England manager, who was given a vote of confidence by his players in a statement before the Cherries clash, said he has no intention of resigning his position.
Former striker Shearer, who was at the helm during an ill-fated stint as manager when the club were last relegated from the top-flight in 2009, believes McClaren is only partially responsible for their recent woes.
He said on BBC's Match of the Day programme: "He's (McClaren) in massive trouble, he has to take his fair share of the blame but the whole club is a mess from top to bottom.
"We've seen statements from the chief executive, from the fitness coach saying how fit the players are, from the manager, from the captain and from the players backing the manager.
"Well if that's a performance to say 'we're backing the manager', then they really are in trouble.
"There are no statements of intent on the pitch where it really matters and that's the problem."
Shearer also questioned the team selection against Bournemouth, with multi-million pound striker Aleksandar Mitrovic dropped to the bench in favour of Emmanuel Riviere.
While Mitrovic has only scored five times since his arrival last summer, Riviere has just one top-flight goal in nearly two seasons in the north-east.
Shearer added: "The team lacks character, leaders.
"You've got a £15million striker that you paid for in the summer, (the team) can't score goals, he's sat on the bench. That tells you where the problems lie at Newcastle: everywhere."