National Environment Management Authority has said 1,200 people have been charged with illegal possession of plastic bags since they were banned last year.
Director general Geoffrey Wahungu said Tanzania and Uganda still pose threat to the ban.
"The two countries have not imposed a ban despite a law by the East Africa Legislative Assembly requiring so. Bags pass through their borders. Only Rwanda, besides Kenya, has effected the ban," Wahungu said in Mombasa on Friday.
He said Busia border is the most porous. “Mombasa’s problem is not as big,” Wahungu said.
Last week, Nema officials in Mombasa seized 17 bales containing millions of plastic bags that came from Dar es Salaam.
Nema county director Steven Wambua summoned the management of Simba Coach that ferried the consignment.
"The conductor faces Sh100,000 fine. The case is ongoing," Wahungu said.
One of the conductors, Mbwana Mzee, paid the fine after pleading guilty to the charge before senior resident magistrate Patrick Wambugu.
Mzee told the court he was unaware that the parcel he was given to load onto the bus comprised plastic bags.
"I am a conductor and only found the parcel I was given was polythene paper at the border point when police inspected the bus. I can pay the fine," he said.
The other conductor pleaded not guilty. Wambua says his officers were acting on a tip-off that the cargo was being imported into the country by a bus company plying the Mombasa-Dar es Salaam route.
"We arrived at the bus station at around 8pm on Friday and impounded the 17 bags. We waited for about three hours but the owner did not show up," he said.
Wambua said the cargo owner is still at large. Wahungu said there is overwhelming compliance with the ban. He also said demolition of structures sitting on riparian land will not stop.
Wahungu said pulling down buildings in Mombasa will begin when the county’s regeneration team is ready.
The director general spoke on Friday in Mombasa during the “Environmental Campaign” launch spearheaded by the Kenya Conference of Catholic Bishops.
The programme targets planting of 10,000 trees with two weeks in Mombasa.
Bishop Martin Kivuva said they were responding to Pope Francis’ letter of May 2015 on the environmental conservation. "Tree cutting has affected our water towers," he said.
Wahungu said 25 million trees were planted last year.
"The overall objective is to reach 10 per cent tree cover by 2022. The government reversed the deadline downwards from 2030," Wahungu said.
Elsewhere, the ban has affected polythene tubes, which are key in seedling production, Migori’s Kenya Forest Service county ecosystem conservator George Abuto has said.
He was speaking on Wednesday at Migori Teachers Training College during the launch of the 2018 short rains tree planting.
"Before the ban, we could produce 10,000 tree seedlings, but now we hardly get 5,000 seedlings," Abuto said.