Taiwan's Tingyi - which operates the instant noodle and beverage Master Kong brand in China - struck the deal with PepsiCo earlier this month.
A worker taking part in the action told the BBC staff were "taking leave together" to defend their legal rights.
A spokeswoman from PepsiCo said that their contracts would be honoured.
In a brief statement, a Pepsi spokeswoman in Beijing said: "PepsiCo is a responsible employer. We have high commitments on our staffers' rights."
"We are holding positive communications with our employees."
Tingyi struck a deal with Pepsi on 4 November to buy out PepsiCo China's bottling division.
Media reports in China suggest that the deal has aroused widespread discontent, and workers from five factories in Chongqing, Chengdu, Fuzhou, Lanzhou and Nanchang have decided to walk out.
There are a total of 24 bottling factories in China run by PepsiCo, which employ some 20,000 workers.
PepsiCo China did not say how many workers were taking industrial action, but a Sina Weibo page said to be put up by workers from the southern city of Fuzhou said 1,100 people there had taken leave to join the protest.
An operator for another page on Sina Weibo - China's equivalent of Twitter - which claims to be representing workers in the central Chengdu factory told the BBC that some 500 staff members were "on leave", equivalent to half of the factory's workforce.
Chinese newspaper the Economic Observer reported that under the tie-up PepsiCo workers' contracts will be terminated and they will have to negotiate new terms with the joint venture.
Many of the protesters believe this will be disadvantageous to them, according to the report.
But the PepsiCo China statement said: "Our deal with Master Kong is yet to receive government approval.  Once it is approved, labour contracts that belong to the bottling cluster will still be honoured."
The Chengdu PepsiCo factory worker told the BBC via Sina Weibo that the protesters were defending their legal rights.
"To us, Pepsi is not just a job that we keep in order to feed our family, it is a career that we all work hard to pursue."

Jamie Frater, 43, was jailed for life in 1993 for the murder of teacher Geoffrey du Rose in Bournemouth.
He went on the run after failing to return to prison in 2012, but later gave himself up. He also absconded from open prison in 2001.
Members of the public are being advised not to approach Frater, who "could present a risk to the public".
Det Supt Jez Noyce, of Dorset Police, said: "There may be various reasons why he has not complied with his release from prison licence conditions and I appeal to him directly to make contact with police at the earliest opportunity.
"I'd like to assure members of the public that officers are making every effort to find this man as soon as possible".
Frater was convicted stabbing Mr du Rose when the teacher chased him from the garden of his home following a robbery at a nearby shop.
He is described as white, of medium build, 5ft 8ins tall, with short, receding, brown hair.
Workers from at least five PepsiCo bottling factories in China are taking part in protests against a takeover deal.
[NEXT_CONCEPT]
A convicted murderer missing from Dorset is wanted by police after he breached his licence conditions.