My website is served with IP address instead of domain name in some search engines

So the search engines crawl the web. They can either discover your site via crawling or you registering the site. Now depending on how the site was referenced, by IP or DNS, this will impact the crawling and subsequent links. This can also occur if a link in your own website refers to the website by IP.

To solve this, however it got leaked, is to ensure the website always redirects from an IP based URL to a DNS based URL. Once fixed, the search engines will eventually catch up. I am not aware if there are ways to sign up at each as the owner and fix the data.

One way to solve this, if you are using a Linux host, would be to add a rewrite to the htacces file like this (update to your IP):

RewriteEngine On
RewriteBase /
RewriteCond %{HTTP_HOST} ^12\.34\.56\.789$
RewriteRule ^(.*)$ http://www.yourdomain.com/$1 [L,R=301]