This is differentiated from GO (P), Government Order (Printed) and GO (Rt), Government Order (Routine). See this list of abbreviations:
http://trivandrum.gov.in/~trivandrum/index.php/citizennservi...

Here is an example:
© GOVERNMENT OF TAMIL NADU 2012
Manuscript Series
G.O.No.362, Dated 5th October 2012 [...]
ORDER:
In the Government Order first read above, orders were issued sanctioning revised rate of Dearness Allowance to State Government employees as detailed below"
http://www.tn.gov.in/gosdb/gorders/finance/fin_e_362_2012.pd...

I have not found an explicit explanation of "manuscript", but the distinction from GO (P) suggests that it means an order that may not be literally written by hand, but has not (yet) been printed in the Official Gazette.


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Note added at 2 hrs (2013-01-18 09:01:51 GMT)
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I do not think this term has anything to do with the normal meaning of "manuscript", meaning "written by hand". Probably its historical origin lies in a distinction, in the colonial period, between handwritten and printed public documents, but orders in the "Manuscript series" are printed nowadays, as many examples on the Internet show. It seems to be just a name.

The following quotation from a Tamil Nadu government manual on administrative procedures gives a clue to what it means in practice. It is on p. 60 of the file:

"131. Before deciding on the nature of the disposal which any paper should receive, the period for which it need be retained should always be a matter for consideration, and the practice of recording papers of no permanent interest in the 'Manuscript Series' should be avoided as far as possible. Any Government Order which lays down a policy, or which introduces some new features or departure is rightly indexed in the 'Manuscript Series', "subsequent orders which are based on these or appeal to these for authority but do not depart from them are a matter of not permanent nature and consequently either 4 Decennium Series or 3 Decennium Series or 2 Decennium Series or Decennium Series or 'Routine' series are the proper disposal for these"
http://www.tn.gov.in/acts-rules/pandar/par_SOM.pdf

This suggests that in Tamil Nadu "Ms." (Manuscript) is used to classify major new orders and subsequent related orders are classified as "D", 2D", "3D" or "4D". I have not seen references to "Printed" government orders in Tamil Nadu, so perhaps they do not use that category there.

The great majority of Tamil Nadu government orders are classified as Ms., and a few as D, 2D, 3D or 4D. I have not seen any other categories used in Tamil Nadu. There are a few orders that are just "G.O.", with no code following. I have not looked at all the lists, but here they are:
http://www.tn.gov.in/gosdb/viewdepartments.php

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Note added at 2 hrs (2013-01-18 09:02:28 GMT)
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It would probably be better to express this as "Government Order (Manuscript Series)".