The corporation, which produces Pobol y Cwm for the Welsh-language channel S4C, conducted a "detailed review" after the Welsh government complained.
Ministers claimed an episode about bovine TB broke editorial guidelines and they were denied a right of reply.
But BBC Cymru Wales has not upheld the complaint.
During the episode - seen last week by 33,000 viewers - one of the characters accuses the Welsh government of not having the "backbone" to cull badgers and of not caring about the countryside.
But in another scene, other characters gave an opposing point of view, saying farmers were to blame for the spread of TB in cattle.
BBC Cymru Wales said its review had looked at the episode in question and others that have been carrying the same storyline over a number of months.
"As a popular soap, Pobol y Cwm always aims to deal with sensitive and controversial issues in an accessible and balanced way," it said in a statement.
"Following our review, we are satisfied that a number of different viewpoints about Bovine TB eradication were discussed both within the individual programme and throughout the series run.
"We have concluded that our approach to this important issue was both balanced and impartial, complying with the BBC's editorial guidelines.
"On that basis we have not upheld the complaint."
A Welsh government spokesman said: "We can confirm we have received a letter from BBC Cymru Wales and will be considering their response."
In addition to the complaint, the Welsh government had asked S4C to pull a repeat of the episode and remove it from the S4C online service Clic.
But it was broadcast as planned by S4C, which said the programme included a variety of viewpoints.
An episode of a TV soap opera which featured criticism of a Welsh government decision not to cull badgers was balanced, BBC Cymru Wales says.