"Envoys should follow government's directives and maintain diplomatic decorum," Minister for Defence Bhim Rawal told reporters here.
In a late night development, Nepal yesterday recalled Upadhyaya over charges of non-cooperation and indulging in anti-government activities.
Upadhyaya, a leader of opposition Nepali Congress who was appointed as Nepal's envoy to India in April last year, is being seen as the first casualty of the cancellation of Nepalese President Bidhya Devi Bhandari's planned visit to India.
He has been accused of being involved in toppling the government, breaching his jurisdiction without informing the government and visiting some western Nepal districts accompanying India's ambassador to Nepal Ranjit Rae, Rawal said.
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Rawal said the cancellation of President Bhandari's trip to India has no connection with the government's decision to recall Upadhyaya.
The president was occupied with some unavoidable tasks like announcing the policy document of the government in the Parliament on Monday due to which the visit was cancelled, he said.
"The government has informed India to postpone the visit for now," he said.
"We have informed that the President will pay a visit at an appropriate time to be fixed diplomatically," he was quoted as saying in a Kathmandu Post report.
According to the report, Thapa said Upadhyaya's "recall was made in a bid to strengthen the existing relations between the two nations" but did not explain what the envoy failed to do to strengthen the ties.