The loss is equally worrying because the BJP has gained two seats (to take its total to four) in the state that returns 14 MPs.
The AGP, which had won two seats last time, secured only one this time.
The Congress retained five seats which it had won in the last polls and wrested two from the AGP, while suffering humiliating defeats in three prestigious seats -- Silchar, Tezpur and Gauhati which it had won in 2004 with considerable margins.
The worst loss for the party was Union Minister Santosh Mohan Dev, who was aiming for an eighth term in Parliament, from Silchar.
He was relegated to the third position behind BJP's Kabindra Purukayastha and nascent regional party Asom United Democratic Front AUDF President Badruddin Ajmal.
Another prominent loser for the Congress was controversial lottery baron Mani Kumar Subba who was defeated by AGP MLA Joseph Toppo by 32,542 votes in Tezpur with the seat being the only one won by the regional party.
The BJP which had allied with the AGP doubled its tally to four this time retaining Mangaldoi and Nowgong seats and gaining the prestigious Silchar and Gauhati seats.
The Gauhati seat which was wrested by the Congress in 2004 from the BJP was regained by the saffron party's Bijoya Chakravorty who defeated Congress' Capt Robi Bordoloi, the son of Assam's first chief Minister and Bharat Ratna awardee Gopinath Bordoloi, by 11,809 votes.
The BJP, which has been present in the state since 1990s, finished second in Jorhat and third in Karimganj and Autonomous (ST) District.
The AGP, however, failed to capitalise on the alliance losing two seats it had won in 2004 -- Lakhimpur and Dibrugarh-to the Congress.
The loss in the Assam polls, both for the Congress and its rivals, was due to the emergence of AUDF, which won the Dhubri seat, finished a close second in Silchar and Karimganj and third in Barpeta, Mangaldoi, Kaliabor and Nowgong.
The party, which was formed prior to the last assembly polls in 2006, contested nine seats with its President Badruddin Ajmal and his brother Sirajuddin Ajmal, both MLAs in the state assembly contesting two seats each, and was successful in winning a sizable chunk of the minority votes, a traditional support base of the Congress.
‘AUDF spoiler in AGP result’
Opposition Asom Gana Parishad (AGP) today admitted that Assam United Democratic Front (AUDF) has emerged as the deciding factor in the state's Lok Sabha polls.
"AUDF has been a major factor in the election result and a reason for the losses suffered by AGP-BJP combine and the ruling Congress," AGP President Chandra Mohan Patowary told reporters here.
Out of 14 LS seats in Assam, AGP bagged one seat. AGP candidate Joseph Toppo won Tezpur LS seat by defeating lottery baron and Congress candidate Mani Kumar Subba by more than 32 thousand votes.
The party, however, lost Lakhimpur and Dibrugarh LS seats to Congress which they had won in 2004.
Denying that AGP's seat sharing agreement with BJP had failed, Patowary said both the parties had won five seats jointly which was "a good result".
AGP president admitted that the presence of AUDF, a party primarily belonging to the minority community, had affected the poll prospects of other parties.
He rejected media reports that AGP failed to get minority votes as it aligned with BJP. "There is no substance in this theory as the members of the minority community will at any case vote for AUDF", he said.
BJP has won 4 LS seats in Assam.