I think it just refers to an accountant in general – one of my underlings thinks it is more generally used for a nitpicker.
What say you?
I vote accountant.
Accountant.
There’s a difference?
Another vote for Accountant.
Yep, accountant. One who, in ye olden dayes, would count the beans (and flour and cheeses and cloths and turnips) to make sure the household accounts were in order and no one was stealing from the missus.
I have no idea if that’s the actual etymology, but that’s how it works in my head.
Accountant.
Yup, that’s what I thought.
Thanks, all.
Accountant, with the additional implication of petty beaurocrat.
More seriously than my former response, I think it can be used a couple of ways:
“I like your idea, but we’ll have to run it past the bean counters” (= Have the accountants sign off on it)
“I like your idea, but the Chief will never sign off on it. He’s a real bean counter.” (= Miserly petty bureaucrat)
Just a side note: the term only shows up(so far) in print around 1975.
If I had to guess, it was used by someone who had a memory of the old-time “how many beans in a jar” contest, and the person who had to count them to affirm who won the contest.
You funny man! 
An accountant, especially a nit-picking one, unless it can be demonstrated that an effective account need not be a nit-picker.
Put me in the group who thought accountant.
Hee. I’m something of an accountant, so my father found it quite amusing when I won the “count the jellybeans in the jar” contest at a party. 
An accountant, usually in the context of assessing the financial data (costs, in particular) of a subject without regard to its other aspects.
Damn, I read it as “Bean Eater” and was ready to flame you guys!
Emphasis added. The technology company that currently issues my paycheck is run by bean counters. I mean this pejoratively, in that they know how to count money, but they don’t know how to lead or inspire people, they don’t know how to develop or market product, they don’t know how to organize the workforce, they don’t know how to plan more than one quarter ahead… They can count beans, period.
I didn’t realize it only referred to an accountant.
The other day my husband was yammering on and on about how we could save a couple of dollars every month in electricity by doing some random thing (can’t remember what.)
I rummaged in the cupboard, grabbed several different cans of beans, placed them in his arms and advised him to get counting.
(No, he didn’t get it. And Yes, I personally thought I was hilarious.)