...
if form.validate_on_submit():
        if otdel==0 or otdel is None:
            flash('Выберите отдел!')
        sql_login='SELECT login,password FROM Employee WHERE login="'+str(login)+'"'
        for i in db.engine.execute(sql_login):
            cnt=cnt+1
        if cnt!=0 and cnt==1:
            psw=i.password
            if psw==pas:
                return redirect(url_for('main'))    
            else:
                flash('Неверный пароль! Проверьте правильность введенного пароля.')
        elif cnt>1:
            flash('Введенный логин не уникален!!!')
        else:
            flash('Неверный Логин!')
    else:
        print(form.errors)
...

 <form id="login" method="POST" action="{{ url_for('index') }}">
    {{ form.csrf_token }}
    {{ form.login.label }}{{ form.login }}<br>
    {{ form.password.label }}{{ form.password }}<br>
    {{ form.filial.label }}{{ form.filial }}<br>
    {{ form.otdel.label }}{{ form.otdel }}<br>
    {{ form.submit() }}<br>
</form>

 @app.route('/',methods=['GET', 'POST'])
def index():

 ...
<form id="login" method="POST" action="{{ url_for('index') }}">
    {{ form.csrf_token }}
    {{ form.login.label }}{{ form.login }}<br>
    {{ form.password.label }}{{ form.password }}<br>
    {{ form.filial.label }}{{ form.filial }}<br>
    {{ form.otdel.label }}{{ form.otdel }}<br>
    <input type='submit' value='Войти' />
</form>
...