Craig Cathcart (knee injury) and Miguel Britos (suspended) are also out but the manager singled out Kaboul as the player Watford could miss the most on the weekend.
"He knows my idea and is a player with fantastic leadership. He's an important player in our squad but now is the moment to find another solution," Silva told the club website (www.watfordfc.com).
Silva could add loan signing Molla Wague into the squad to potentially partner Christian Kabasele or Adrian Mariappa in central defence.
"Of course (he comes into contention)," Silva said of the 26-year-old who arrived on a season-long loan from Italy's Udinese and has not played for Watford yet.
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"It's not the best way, as he only worked with us since last Friday. Normally we like to give him time to know our style of play, our idea.
"Maybe we don't have time for that. Between him, Mariappa and Kabasele, I have to choose the centre-backs..."
The manager said he could also call on midfielder Roberto Pereyra who has missed three games this season while defender Kiko Femenia has returned to full training after a head injury.
Watford, who have eight points from four games this season, have not won against Manchester City in the Premier League, losing four of their past six meetings.
City have made a strong start to the season, gathering 10 points and are behind early leaders Manchester United on goal difference.
(Reporting by Shrivathsa Sridhar in Bengaluru; editing by Amlan Chakraborty)
