Vande Bharat Express is capable of attaining a speed of 200 kmh, will cut down the travelling time between the two stations by over five hours.
At present, the Train-18 with all modern facilities for a comfortable journey runs at a maximum speed of 160 kmph between Delhi and Varanasi.
A minor fire was detected in the transformer of C-7 coach, the temperature of which was found to be 90 degrees centigrade, sources said.
Critics have attacked BJP, saying the move is aimed at gaining political mileage in UP ahead of the Lok Sabha elections.
An official said a shower of ballast came flying towards the train near Achalda in Uttar Pradesh when the Dibrugarh Rajdhani, crossing on the adjoining line, run over a cattle.
Investigation into several incidents of the sort in Delhi established that most of the stone-pelters were young children.
The Congress President had attacked the Make in India campaign and Prime Minister Modi after the Vande Bharat Express suffered a snag on its maiden return journey on Saturday.
While travelling from Delhi to Varanasi on Sunday, the train was delayed by 1.25 hours. On its return journey, it was delayed by 1.48 hours, officials said.
The Union Minister said the modern coach factory in Rae Bareli, which is the Lok Sabha constituency of his mother Sonia Gandhi, is a live example of how Congress makes empty promises.
"Vande Bharat Express left Delhi for Varanasi today morning on its first commercial run. Tickets sold out for the next two weeks already. Get yours today!" tweeted Railway Minister Piyush Goyal.
Train 18, as it was formerly called, broke down about 194 km away from Delhi and 18 km away from Tundla railway station in Uttar Pradesh.
The train was ultimately late by more than six hours due to a mechanical fault and reached the destination by 1 pm on Saturday.
Once India's fastest, the Gatimaan Express, which runs between Delhi and Agra with a maximum speed of 160 kmph and an average of 112 kmph, has now receded to the second place.
The semi-high speed train was returning from Varanasi after it was flagged-off by Prime Minister Narendra Modi at New Delhi railway station on Friday.
Vande Bharat Express inauguration despite Pulwama attack, befitting reply to terrorists: Piyush Goyal
Forty CRPF personnel were killed and five injured on Thursday when a Jaish-e-Mohammed suicide bomber rammed a vehicle carrying nearly 300 kg of explosives into their bus in Pulwama district.