You could use the ScriptManager.RegisterClientScriptInclude method:
ScriptManager.RegisterClientScriptInclude(
updatePanel,
updatePanel.GetType(),
"a_key",
"myScript.js"
);
Note that this method will render your script early in the HTML, so your script should not rely on the order scripts are rendered on the page.
More about this method at http://msdn.microsoft.com/pt-br/library/bb337005.aspx
But if your script depends on some other script, a better option is to use the ScriptManager.RegisterStartupScript method, but instead of passing the script body as a parameter, you pass the entire <script> tag with your script's address:
ScriptManager.RegisterStartupScript(
updatePanel,
updatePanel.GetType(),
"a_key",
"<script type='text/javascript' src='my_script.js'></script>",
false
);
Note that the last parameter, which sets the addScriptTags flag, is set to false, allowing you to render the entire tag with the src attribute defined.