At a function held at Rail Bhavan here, Prabhu flagged off the new train services between North Lakhimpur and Murkongselek in Assam and between Balipara in Assam and Bhalukpong in Arunachal Pradesh, an official statement said.
The programme was organised through video-conferencing between Rail Bhavan, Murkongselek and Bhalukpong.
In Delhi, Minister of State for Railways Manoj Sinha, Rajya Sabha member from Assam, Bhubaneswar Kalita, Railway Board Chairman A.K. Mital, Railway Board Member Engineering V.K. Gupta were among those present.
Youth Affairs and Sports Minister Sarbananda Sonowal was present in Murkongselek, while Minister of State for Home Affairs Kiren Rijiju was in Bhalukpong.
Prabhu also inaugurated the daily Guwahati-Murkongselek Intercity Express and the Dekargaon-Bhalukpong Passenger.
The Rangiya-Rangapara North Passenger was extended up to Dekargaon, while the Dekargaon-Harmuti Passenger was extended to Murkongselek.
Stating that it was a "golden day" in the history of Arunachal Pradesh, as the state got its second broad gauge connectivity with the commissioning of the Balipara-Bhalukpong gauge conversion, Prabhu said state capital Itanagar was provided with rail connectivity with Delhi through a direct train earlier this year.
"I am sure this rail connectivity will bring prosperity in the lives of people of this state. This will also serve the defence needs of our country."
The commissioning of the North Lakhimpur-Murkongselek section marked the completion of the Rangiya-Murkongselek gauge conversion project running along the north bank of the Brahmaputra.
The 510-km gauge conversion project costing about Rs.3,600 crore was sanctioned in 2002-03.
According to Prabhu, the project suffered delay mainly due to funds constraint in the past. But in 2014-15, an outlay of Rs.713 crore was provided and the balance Rs.300 crore was provided in 2015-16.
To augment the railway network in the northeast, 13 new lines, three gauge conversion and four doubling projects with balance fund requirement of Rs.37,000 crore have been taken up.
These projects would augment the network in the region by 1,915 km, he said.
Rail connectivity to the northeast has been made a mission item by the government "as we provided an all-time-high budget allotment of Rs.5,200 crore to the projects in this region in 2014-15, which is over 50 percent more than in 2013-14".
"This tempo has been maintained in 2015-16 also by providing Rs.5,300 crore."
Stating that Prime Minister Narendra Modi has always emphasised on developing infrastructure in the northeast, he said: "We will continue to have the best ever relationship with all the eight sister states."
Prabhu said only the capitals of Assam and Arunachal Pradesh were on the broad gauge network while the Tripura capital was connected with metre gauge.
"While Agartala is all set to be on the broad gauge network by March 2016, it will be our endeavour to connect the state capitals of Nagaland, Mizoram, Manipur and Meghalaya by rail with the rest of the country in the next 5-7 years," he said.
He said the railways has been commissioning about 133 km of broad gauge track every year in the northeast in the last 4-5 years.
"In 2014-15, a record was made when about 450 km of lines were commissioned. This year again, we are all set to achieve a new record of commissioning of about 550 km of broad gauge lines in this region."
He said the Bogibeel bridge over the Brahmaputra near Dibrugarh in Assam was also progressing well and its completion in June 2017, would change the landscape of the area.
Sinha said it has been the important priority of the government to develop best possible infrastructure in the northeast.
"Indian Railways is committed to provide better railway connectivity in the region. Indian Railways has really completed these significant gauge conversion projects which have made possible flagging off of new trains today in this area," he said.
Mital said the entire metre gauge section in the northeast would get replaced by broad gauge by March 2016, and except Sikkim, all other states would have broad gauge connectivity in this financial year.