The group, which controls large parts of both regions, is pressuring leaders of local villages to make sure teenagers join its ranks, according to the governor of Bay region, Ali Wardhere Doyow.
"They have been holding meetings for clan elders and told them to meet specific numbers of recruits they want collected from clans," Doyow told VOA's Somali Service.
Doyow said many families and their children have fled their villages to larger towns in the Bay region, including Baidoa, Dinsor and Bardale.
Abdishakur Yaqub Ibrahim, a regional lawmaker who lives in Baidoa, told VOA that dozens of children between the ages of 9 and 18 have fled Shabab-ruled areas in Bay and Bakool over the past few days. He said some of those who fled are his relatives, including a cousin and nephews.
"I now have 14 such kids who fled who are living in my home; some came to me because they are relatives, some are my clanmates," he said.
"Three weeks ago, they called the elders and school leaders and said they want the younger boys. They told the elders that the boys will be educated and trained and that they will then fight against the apostates and Mukhtar Robow."
Robow is al-Shabab's former deputy emir and a Bakool native who defected to the government in August. There are reports that Robow is planning to return to the region to mobilize locals against his former militant group.
Ibrahim says the group is targeting families who have sons.
"They told the elders that if a family has two sons, they will draft one as a militant; if they have three, they will take two of them," Ibrahim said. "They are saying they will educate the children, but they are going to turn them into bombs."
THOSE WHO FLED
Human rights groups have previously accused both al-Shabab and pro-Somali government forces of using child soldiers. Last year, the U.N. Children's Fund estimated there were at least 5,000 underage soldiers in the country, most of them recruited into al-Shabab.
The recruiting drive appears to have picked up in recent weeks. Last month, authorities in the coastal town of Adalle reported that more than 100 children who fled a Shabab recruitment campaign in the Galmudug region had arrived there.
Authorities in the town of Bardhere report the arrival of 10 families who fled with their children because of Shabab recruitment efforts in the Gedo region.
One Bay region youngster who fled to Baidoa told VOA he is 15 years old. He said he left his home village after the militants made clear their intention to take him.
"They came to the Quran school, then they went to my father and he told them he will not hand me over. Then I took a motorcycle and I came here to stay with my uncle," said the boy, whose name is being withheld due to concerns for his safety.
VOA also spoke to a 14-year-old boy who arrived Baidoa on September 21, after his parents shipped him out of his village. He said he was the only son in his family.
The boy said al-Shabab raided his school which had about 40 boys. He said he does not know what happened to the other boys.
He said he did not want to become an al-Shabab fighter because they "harm people."
Governor Doyow urged the clans and elders to resist al-Shabab and not "donate" their sons to the militant group.
"Reject, don't let them take away your children. Fight it off," he said.