The West Bromwich East MP said it was "outrageous" and "anti-democratic" that members of Labour's ruling National Executive Committee (NEC) had deselected borough councillors for the upcoming local elections.
The move – described today as "mafioso style politics" – has seen a number of allies of Mr Watson told they cannot fight for their seats.
It has been perceived as an orchestrated attack on the Labour deputy leader and comes after hard left allies of Mr Corbyn seized control of the selection process in Sandwell.
And Mr Watson today warned that the same scenario was happening in other parts of the UK, saying: "If it’s going on here, it’ll be going on up and down the country."
He told the Express & Star: “This is the hard left wreaking retribution on long serving councillors for no reason whatsoever.
"It’s completely anti-democratic and against all normal rules of natural justice.
"This is the kind of brutal factional politics Jeremy has always stood against and it’s very disappointing to see a handful of hard left members of Labour NEC acting in this way.
"Local members have been deprived of their chance to select their candidates and deprived of hard working councillors that have served their communities dutifully for many years.
"This situation is outrageous and I’ll be raising it urgently with the Chair of Labour’s NEC in the strongest possible terms.”
Around a quarter of the councillors up for election this year have been deselected, including half a dozen allies of Mr Watson.
They include the mayor Joy Edis, who represents Friar Park; deputy mayor and Bristnall councillor Carol Goult; Great Barr councillor Shirley Hosell; Newton councillor Dave Hosell, who is the cabinet member for highways; Hateley Heath councillor Pat Davies; and Smethwick councillor Keith Davies, who is a former mayor first elected in 1986.
The NEC's selection panel for candidates is said to have included Momentum-backed activist Rachel Garnham and UNITE regional officer Frank Keogh.
A source close to Mr Watson said: “These deselections are part of an orchestrated attack on Tom Watson by the hard left at the top of the Labour Party.
"It’s pretty shocking mafioso style politics to deselect good local councillors as a way to harm Tom. So much for kinder gentler politics under Jeremy Corbyn.”
Former council leader Steve Eling has also been deselected in Abbey ward, having been suspended by Labour's NEC in January following an unspecified complaint.
A spokesman for West Midlands Labour said: "We have a fantastic set of energetic and enthusiastic candidates who share a positive vision for our area."