"The quote and unquote elections in the eastern part of the country this past Sunday are an unfortunate and counterproductive development," Ban said in a speech.
"I urge all parties concerned to urgently recommit to full implementation of the letter and spirit of the Minsk protocol and memorandum designed to bring peace and stability to all of Ukraine," he added.
He said that the crisis, involving "the tragedy of lost lives both in land and in the sky… risks jeopardising our collective ability to solve… problems."
The elections of leaders in two unrecognised statelets in eastern Ukraine on Sunday were backed by Russia but condemned by the Western-backed Kiev government, the United States and EU powers.
Ban had said last week that the elections would "seriously undermine" the Minsk peace agreements struck in early September, which have also been threatened by continued violations of a truce.
Ukrainian President Petro Poroshenko was to meet security chiefs Tuesday to "re-examine" the peace accord following what he called the "pseudo elections".
On Tuesday Ban also commended the Organization for Security and Co-operation in Europe (OSCE) for its "early and active engagement and its prominent role on the ground" in Ukraine.
Ukraine's SBU security service has criticized Austrian former far-right politician Ewald Stadler, who led a group of unofficial 'election observers' into the separatist-held territory from Russia.
The SBU said they were "illegally supporting guerillas and terrorists".