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Sam Ongeri summoned European Union ambassadors on Monday to express his "utmost displeasure" at what he claimed was an "orchestrated attempt by a number... to influence the way Kenyans conduct their forthcoming elections."
The March 4 polls are the first since bloody post-election violence five years ago, when what began as political riots quickly turned into ethnic violence that killed some 1,200 people and displaced 600,000 others.
"The remarks made by EU envoys are clearly inflammatory and could have the effect of polarising the country," Ongeri said in a statement after the meeting.
Local media recently quoted various EU ambassadors as saying they would avoid meeting with presidential candidate Uhuru Kenyatta and his running mate William Ruto, who both face trial at the International Criminal Court (ICC).
Kenyatta, the deputy prime minister and son of Kenya's founding president, faces trial on April 11 for his alleged role in orchestrating murder, rape and violence after the 2007 polls.
EU ambassadors issued a joint statement after the meeting in which they "rejected any allegation of interfering in the elections process" adding that "it is for the Kenyan people to elect their leaders."
However, the EU statement noted they "and other like-minded states have a long-standing policy, not limited to Kenya, to have only essential contact with indicted ICC suspects."
It added that the EU "supports an end to impunity and supports the rule of law" in Kenya.
"Regardless who is elected president, cooperation with the International Criminal Court is of vital importance to create accountability for political violence and build a stable Kenya," the statement added.
The comments come ahead of Kenya's first ever live presidential debate between the candidates due to start later on Monday.
Last week Johnnie Carson, the top US diplomat for Africa, warned Kenyans that "choices have consequences", in an apparent caution over the possible victory of Kenyatta.
"We live in an interconnected world and people should be thoughtful about the impact their choices have on their nation, economy, region and the world in which they live," he told reporters, without naming any names.