回答ありがとうございます。

フォーラムで過去ログを確認したのですが、
DBのCharsetが以下のようになっていることが原因だと考えられますか？

MariaDB [(none)]> show variables like 'char%'
-> ;
+--------------------------+----------------------------+
| Variable_name | Value |
+--------------------------+----------------------------+
| character_set_client | utf8 |
| character_set_connection | utf8 |
| character_set_database | latin1 |
| character_set_filesystem | binary |
| character_set_results | utf8 |
| character_set_server | latin1 |
| character_set_system | utf8 |
| character_sets_dir | /usr/share/mysql/charsets/ |
+--------------------------+----------------------------+

TNKさん、広瀬さん、
回答ありがとうございました。解決しました！

画面とDBがutf-8なので、送信時もutf-8でやればいいのでは？
と思い、以下３点をutf-8で扱うよう変更しました。

・mb_internal_encoding
・class PHPMailer_JP extends PHPMailer {
public $CharSet = "UTF-8";
public $Encoding = 'base64';
}
・$mailer->Body = $MAIL_MESSAGE;

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mb_language("japanese");
mb_internal_encoding("UTF-8");
require("phpmailer/class.phpmailer.php");

/* setting */
$MAIL_FROM = "zabbix@iotapbatch01";
$MAIL_FROMNAME = "Zabbix 障害通知";
$MAIL_SMTP_HOST = 'せんどぐりっど';
$MAIL_SMTP_USER = 'ゆーざー';
$MAIL_SMTP_PASS = 'ぱすわーど';
/* setting */

$MAIL_TO = $argv[1];
$MAIL_SUBJECT = $argv[2];
$MAIL_MESSAGE = $argv[3];

class PHPMailer_JP extends PHPMailer {
public $CharSet = "UTF-8";
public $Encoding = 'base64';
}

$mailer = new PHPMailer_JP();
$mailer->IsSMTP();

$mailer->Host = $MAIL_SMTP_HOST;
$mailer->SMTPAuth = true;
$mailer->Username = $MAIL_SMTP_USER;
$mailer->Password = $MAIL_SMTP_PASS;

$mailer->From = $MAIL_FROM;
$mailer->AddAddress($MAIL_TO);

$mailer->FromName = mb_encode_mimeheader(mb_convert_encoding($MAIL_FROMNAME,"ISO-2022-JP-MS","UTF-8"),"ISO-2022-JP-MS");
$mailer->Subject = mb_encode_mimeheader(mb_convert_encoding($MAIL_SUBJECT,"ISO-2022-JP-MS","UTF-8"),"ISO-2022-JP-MS");
$mailer->Body = $MAIL_MESSAGE;
// $mailer->AddReplyTo($email, $from);

if(!$mailer->Send()){
print "failed: " . $mailer->ErrorInfo . "\n";
}else{
print "success" . "\n";
}

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