Finally, I can find a solution for this. This can be done by setting the headers in InitiateMultipartUploadRequest , as shown below:
InitiateMultipartUploadRequest initRequest = new
InitiateMultipartUploadRequest(bucketName, keyName);
initRequest.putCustomRequestHeader("x-amz-server-side-encryption", "aws:kms");
initRequest.putCustomRequestHeader("x-amz-server-side-encryption-aws-kms-key-id", kmsKey);
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