UP and Bihar contributed 105 seats to the BJP's tally in 2014.
It has now lost 8 Lok Sabha by-polls in the last four years, including three successive losses in UP and two seats in Rajasthan.
Archis Mohan reports.
The bypoll results of four Lok Sabha and 10 assembly seats across 11 states have caused murmurs of discontent in the Bharatiya Janata Party-led National Democratic Alliance.
The results also had leaders of the Telugu Desam Party and Aam Aadmi Party discover redeeming features in the Congress.
The Janata Dal-United, the BJP's ally in Bihar, which lost the Jokihat assembly seat to the Rashtriya Janata Dal, fumed at the increasing fuel prices.
Shiv Sena chief Uddhav Thackeray threatened that his party would fight all future elections on its own, and accused the BJP of rigging the Palghar Lok Sabha bypoll.
Maharashtra Chief Minister Devendra Fadnavis said he would talk to Thackeray to convince him to keep the BJP-Sena alliance intact for the 2019 Lok Sabha elections.
The JD-U's loss suggested an erosion in Bihar Chief Minister Nitish Kumar's support base and increasing acceptance of the RJD under Tejashwi Yadav.
The JD-U defeat could spur desertions of its Yadav and Muslim legislators.
Meanwhile, Andhra Pradesh Chief Minister Nara Chandrababu Naidu said the Congress was a better bet than the BJP at the current juncture.
The TDP, Naidu said, had fought the anti-federal Congress governments of Indira Gandhi and Rajiv Gandhi, but now the situation was much worse.
Delhi Chief Minister Arvind Kejriwal, also the Aam Aadmi Party chief, tweeted how people were 'missing an educated prime minister like Manmohan Singh. It is dawning on people now.'
'The PM, after all, should be educated,' Kejriwal tweeted and attached an article on steep fuel prices.
In Lucknow, Samajwadi Party chief Akhilesh Yadav too acknowledged the support of the AAP, along with that of other Opposition parties, for the Kairana Lok Sabha and Noorpur assembly wins. The Rashtriya Lok Dal's Jayant Chaudhary also thanked the AAP.
Communist Party of India-Marxist General Secretary Sitaram Yechury said the bypoll results weren't just about the unity of secular forces. The results, he said, also show that the BJP vote share had declined substantially from 2014.
"It is a big setback to the BJP-RSS (Rashtriya Swayamsevak Sangh) as UP and Bihar gave them an absolute majority," Yechury said.
The BJP clearly has a problem on its hands.
Uttar Pradesh and Bihar contributed 105 seats to its tally in 2014. It has now lost 8 Lok Sabha by-polls in the last four years, including three successive losses in UP and two seats in Rajasthan.
BJP President Amit A Shah has been talking of his party's strategy to offset its losses in the northern Indian states by winning in the north east, West Bengal, Odisha, Telangana and Andhra Pradesh.
The BJP lacks a strong structure in the southern states.
In Odisha and Bengal, it is faced with strong regional leaders.
The entire north east sends 25 seats to the Lok Sabha, compared with the 135 of UP, Bihar and Jharkhand.
The BJP failed to wrest from the united Opposition the two assembly seats that had polls in Jharkhand.
For the BJP, more worrying than its losses was its vote share in three of the four Lok Sabha seats -- two in Maharashtra and Uttar Pradesh's Kairana -- were lower than the vote share it had won in 2014 in these very seats.
The BJP's defeats have taken the sheen off the Modi government's celebrations to mark its four years, with questions being asked about increasing fuel prices, agrarian distress and joblessness.
The Modi government hopes to turn the tide in the heartland by reaching out to sections of the OBCs (Other Backward Classes). It has plans to subdivide the OBC category to allocate specific quotas to the most backward castes.
The BJP faces challenging assembly elections by the end of the year in Rajasthan, Madhya Pradesh, Chhattisgarh and Mizoram.
In Madhya Pradesh, the Shivraj Singh Chouhan-led government faces a sustained farmer protest on the anniversary of the Mandsaur police firing.
Within the BJP, leaders tried to put the blame of defeats in Uttar Pradesh's Kairana Lok Sabha and Noorpur assembly seats on the Yogi Adityanath-led BJP government in Uttar Pradesh.
BJP MP Bhartendra Singh said leaders that the party has projected 'seem more like appointees than people's leaders'.
BJP Rajya Sabha member Dr Subramanian Swamy said the 'huge setback' was due to 'hubris', but there was still time to take corrective measures.
