The announcement by LSE, which also operates the Milan stock exchange, is the latest twist in its longstanding attempt to merge with the German stock exchange operator.
The LSE said it had examined the European Commission's request to divest its majority stake in Italian trading unit MTS, concluding it could not commit to such a request.
"The LSEG Board believes that it is highly unlikely that a sale of MTS could be satisfactorily achieved, even if LSEG were to give the commitment," LSE said in a statement.
"Based on the Commission's current position, LSEG believes that the Commission is unlikely to provide clearance for the merger," it added.
The London Stock Exchange did not put an end to the possibility of a tie-up, however, saying it would continue to seek to implement the deal.
Deutsche Boerse, which also operates the Luxembourg-based clearing house Clearstream and the derivatives platform Eurex, confirmed the decision on MTS and said a final decision from Brussels was expected within weeks.
The planned merger has drawn criticism from France, Belgium, Portugal and the Netherlands, fearful for their own stock exchanges, owned by Euronext.
Last month LSE agreed to offload the French arm of clearing house LCH to European rival Euronext, as part of efforts to address EU competition concerns.
LSE said yesterday it viewed the LCH sale an "effective and capable" remedy to competition concerns, deeming the MTS demand "disproportionate".
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