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When calling Athena from a Lambda function, you need to ensure the Lambda function's execution role has permission to access your Amazon S3 buckets. That same logic applies to other ways you can run your code, such as Amazon EC2 or Amazon ECS, and includes both the source bucket and the destination bucket. For example, take a look at the AWS Managed Rule AmazonAthenaFullAccess below. Note that this includes actions like s3:PutObject and s3:AbortMultipartUpload that Athena may use to create temporary files, not just read actions like S3:GetObject or S3:ListBucket.
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Thanks! It was a matter of adding the right permissions to the user's role.
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Where is your python (boto3) code being executed? Lambda? EC2? Fargate?