The FA made fun of Kane's failure to score during his side's 1-2 loss to Manchester United in the FA Cup semi-finals on Saturday, reports Efe.
The since-deleted tweet asked the question: "What's in your pocket, Chris?" referring to Manchester United defender Chris Smalling, who answered "Harry Kane."
An FA spokesman said the organisation had contacted both Tottenham and Man United to apologise.
For its part, Tottenham has declined to comment.
Kane scored 37 goals in 44 matches for Tottenham this season, and the FA Cup represented the last chance for his club to lift a trophy this season.
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