Morton Aaslund on Monday issued a statement along with his counterparts from the UK and the US in which the three countries said they regretted Khartoum's "failure to create a free, fair and conducive elections environment."
In a statement summoning the ambassadors to Sudan's foreign ministry, Khartoum labelled the criticism "blatant interference in the internal affairs of the country."
"The elections are a purely Sudanese affair decided by the Sudanese, and no other party has the right to intervene or express an opinion," a statement said.
The European Union representative in Khartoum was also summoned, the ministry said, without giving details.
EU foreign policy chief Federica Mogherini had said before voting began that the election could not produce a credible result, citing the ruling National Congress Party's failure to attend a meeting with the opposition to
arrange a national dialogue.
Bashir proposed the dialogue last January as a way to resolve the country's economic woes and the conflicts on its peripheries.
The foreign ministry said Sudan was committed to resuming the dialogue after the election results are announced and a new government is formed.
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The polls for the presidency and state and national parliaments were boycotted by the mainstream opposition.
Thirteen little-known candidates are challenging Bashir, after two others withdrew after voting got underway, complaining of irregularities in the electoral process. Results are expected on Monday.
Bashir, 71, is wanted by the International Criminal Court for alleged war crimes, crimes against humanity and genocide in the western region of Darfur.