"to flow" is an intransitive verb so it cannot have a direct object. so we cannot form a passive with an intransitive verb.
Right. Or... mostly right. According to wiktionary.org the verb flow has ten different definitions. Seven out of the ten are intransitive which don't take an object, and therefore having an object in the sentence would be an error.
The other definitions such as "to cover with water or other liquid" allow an object. So, it's a case by case basis. "Input" is not a water or liquid though...
Input was not flowed into the system (By admin) when he called me. So I asked him to wait*
Input did not flow into the system when he called me. So I asked him to wait.
Basically correct. See below for more examples though.
Input was not flowed into the system*
Can we use above sentence as "Window was not opened" or "He was not killed in accident".
No. Because those verbs may have a direct object, and can be passive.
If you prefer to use the passive tense with "flow", then try a different verb:
The input had not been entered into the system (by the admin) when he called me. So I asked him to wait.
Correct. Also "typed in", "submitted".