Hi all thanks for your time and suggestion...
I got the solution. I was applying css on literal's text property in Page_PreRender event.
So that in rendered output of page link was displayed like this: <link type="text/css" rel="stylesheet" href="~/css/skin.css" > so that css path was not getting found.
Solution for this is:
<pre lang="cs">protected void Page_Init(object sender, EventArgs e)
{
//litSkinStyle.Text = Common.auto_version("css/skin.css");
var link = new HtmlLink();
link.Href = Common.auto_version("css/skin.css");
link.Attributes.Add("rel", "stylesheet");
link.Attributes.Add("type", "text/css");
Page.Header.Controls.Add(link);
}</pre>
Now I'm giving relative path which is correctly rendered in output and css is applied.
I used this way because I have done auto version of css.