Based on the error message you gave, it sounds like you are trying to upload a downloaded agent distribution file into the "Update EM Catalog" area in OEM that's available when you are set up with an offline MOS connection. The agent software you downloaded needs to be imported into OEM via EMCLI's "import_update" verb, not through the GUI. That area in the GUI is used to download and update the catalog file which contains a list of patches, agent software, etc, so that OEM knows they exist, but it does not contain the actual patch or agent software.
Gokhan Atil covered this use case very well in a blog post: http://www.gokhanatil.com/2012/03/how-to-download-new-agent-software-for-oracle-cloud-control-12c-in-offline-mode.html
[Edit after seeing Akanksha's response: You may need to use both 'import_update_catalog' and 'import_update' depending on which files you need to load.]
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How are you uploading this zip to OMS. i hope you are using the emcli -
- ./emcli import_update_catalog -omslocal -file=zip file absolute path
Refer this Installing Oracle Management Agent