"Our helicopter couldn't land at the helipad due to poor visibility after we took off from Resubelpara," party general secretary Luizinho Faleiro told IANS.
He, however, said Gandhi proceeded to Shillong by road after the chattered Pawan Hans helicopter landed safely at the Lokpriya Gopinath Bordoloi International Airport in Guwahati.
Gandhi was scheduled to interact with Congress workers in Shillong.
On Tuesday, Gandhi began his two-day campaign by addressing a rally at Hapoli in Arunachal Pradesh's Lower Subansiri district, and another at Resubelpara in Meghalaya's North Garo Hills district.
The Congress vice president was accompanied by Meghalaya Chief Minister Mukul Sangma and Faleiro.
Gandhi will Wednesday visit Wangjing in Thoubal district of Manipur, and address a rally there.
The Congress won both the Outer Manipur and the Inner Manipur seats in the last Lok Sabha elections, and sitting MPs - Thangso Baite and Thokchom Meinya Singh - have been fielded again this time.
Gandhi will also travel to Mizoram on the same day to campaign for party nominee C.L. Ruala.
Arunachal Pradesh, Mizoram and Meghalaya will go to polls April 9, while Manipur will see two-phase polling April 9 and 17.