The Enterprise version of Zoho CRM has 'Page Layouts', which allow you to build different 'pages' for your separate departments or even business units/businesses, which include different fields, layouts and even workflow.
If you are not using the Enterprise version then the easiest way to do this is to add a picklist (drop-down) field on the
opportunity module called 'Business Unit', then build the report on
that as the filter.
There is already a standard pipeline report
in the CRM. This report does not have a business unit filter though so
you can clone this report and then add the filter on the 'Business Unit'
field and name it 'Pipeline report for business Unit A'. The filter for
this would be based on one of the values in the Business Unit field,
for example "Business Unit A".
Then of course you need the report
for "Business Unit B", C, D and so on, so simply clone this report and change the filter
to "Business Unit B" and save as a new report: "Pipeline Report for Business Unit B".
The end result
of this is that you have one pipeline report for the entire CRM (with no
filters) and then additional pipeline reports, each with a filter for
the different business units.